In [2]:
%%bash
cat /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
cat /usr/share/gromacs/top/oplsaa.ff/ffbonded.itp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro
; OPLS atom types and masses. ; Atom types are named opls_X, where X is the OPLS number. ; The opls_ prefix is to avoid users confusing atom types ; (always prefixed) with atom numbers in molecules (never prefixed). ; ; Types 1-134 are from the united-atom OPLS, which can be ; useful for solvents and/or CH2 optimizations (e.g. in lipids). ; Explicit all-atom parameters start with opls_135. ; Note: For UA amide parameters - ; NMA - types 1,2,3,4,7,39 ; Formamide 131,2,12,13 ; DMF 131,2,3,132 ; Acetamide 1,2,7,12,13 ; ; Types 1-65 are united-atom parameters for proteins, ; see JACS 110, 1657 (1988). ; opls_001 12.01100 ; opls_002 15.99940 ; opls_003 14.00670 ; opls_004 1.00800 ; opls_005 14.02700 ; opls_006 13.01900 ; opls_007 15.03500 ; opls_008 13.01900 ; opls_009 14.02700 ; opls_010 15.03500 ; opls_011 12.01100 ; opls_012 14.00670 ; opls_013 1.00800 ; opls_014 13.01900 ; opls_015 14.02700 ; opls_016 14.02700 ; opls_017 12.01100 ; opls_018 15.99940 ; opls_019 14.02700 ; opls_020 14.00670 ; opls_021 1.00800 ; opls_022 14.02700 ; opls_023 15.99940 ; opls_024 1.00800 ; opls_025 13.01900 ; opls_026 12.01100 ; opls_027 14.02700 ; opls_028 14.02700 ; opls_029 13.01900 ; opls_030 13.01900 ; opls_031 14.02700 ; opls_032 32.06000 ; opls_033 1.00800 ; opls_034 14.02700 ; opls_035 32.06000 ; opls_036 15.03500 ; opls_037 14.02700 ; opls_038 32.06000 ; opls_039 15.03500 ; opls_040 14.00670 ; opls_041 1.00800 ; opls_042 14.00670 ; opls_043 12.01100 ; opls_044 12.01100 ; opls_045 12.01100 ; opls_046 14.00670 ; opls_047 1.00800 ; opls_048 12.01100 ; opls_049 12.01100 ; opls_050 12.01100 ; opls_051 14.00670 ; opls_052 1.00800 ; opls_053 12.01100 ; opls_054 14.00670 ; opls_055 1.00800 ; opls_056 14.02700 ; opls_057 14.02700 ; opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester opls_060 13.01900 ; opls_061 14.02700 ; opls_062 15.99940 ; O- in COOR ester opls_063 15.03500 ; CH3 in COOCH3 opls_064 12.01100 ; opls_065 15.03500 ; opls_066 16.04300 ; CH4 JACS,106,6638 (1984) opls_067 15.03500 ; CH3 (C1) ETHANE opls_068 15.03500 ; CH3 (C2) N-ALKANES opls_069 15.03500 ; CH3 (C3) ISOBUTANE opls_070 15.03500 ; CH3 (C4) NEOPENTANE opls_071 14.02700 ; CH2 (SP3) ALKANES opls_072 14.02700 ; CH2 (SP2) 1-ALKENES opls_073 13.01900 ; CH (SP3) ISOBUTANE opls_074 13.01900 ; CH (SP2) 2-ALKENES opls_075 13.01900 ; CH (AROM) BENZENOID united atom opls_076 12.01100 ; C (SP3) NEOPENTANE opls_077 12.01100 ; C (SP2) ISOBUTENE opls_078 15.99940 ; O ALCOHOLS JPC,90,1276 (1986) opls_079 1.00800 ; H(O) ALCOHOLS JPC,90,1276 (1986) opls_080 15.03500 ; CH3 IN METHANOL JPC,90,1276 (1986) opls_081 14.02700 ; CH2 IN ETHANOL JPC,90,1276 (1986) opls_082 32.06000 ; S IN H2S JPC,90,6379 (1986) opls_083 32.06000 ; S IN RSH JPC,90,6379 (1986) opls_084 32.06000 ; S IN RSR JPC,90,6379 (1986) opls_085 32.06000 ; S IN RSSR JPC,90,6379 (1986) opls_086 1.00800 ; H IN H2S JPC,90,6379 (1986) opls_087 1.00800 ; H(S) IN RSH JPC,90,6379 (1986) opls_088 15.03500 ; CH3 IN CH3SH JPC,90,6379 (1986) opls_089 14.02700 ; CH2 IN CH3CH2SH JPC,90,6379 (1986) opls_090 15.03500 ; CH3 IN CH3SR JPC,90,6379 (1986) opls_091 14.02700 ; CH2 IN RCH2SR JPC,90,6379 (1986) opls_092 15.03500 ; CH3 IN CH3SSR JPC,90,6379 (1986) opls_093 14.02700 ; CH2 IN RCH2SSR JPC,90,6379 (1986) opls_094 14.00670 ; N IN CH3CN Mol.Phys.,63,547 (1988) opls_095 12.01100 ; C IN CH3CN Mol.Phys.,63,547 (1988) opls_096 15.03500 ; CH3 IN CH3CN Mol.Phys.,63,547 (1988) opls_097 39.94800 ; Argon from Verlet & Weis Mol.Phys.,24,1013 (1972) For Ne and He, opls_098 83.79800 ; Krypton from Verlet & Weis Mol.Phys.,24,1013 (1972) see types 129,130. opls_099 131.29300 ; Xenon from Verlet & Weis Mol.Phys.,24,1013 (1972) opls_101 14.00670 ; N (NH4+) JPC,90,2174 (1986) opls_102 14.00670 ; N (RNH3+) JPC,90,2174 (1986) opls_103 14.00670 ; N (R4N+) JPC,90,2174 (1986) opls_104 1.00800 ; H (NH4+) JPC,90,2174 (1986) opls_105 1.00800 ; H (RNH3+) JPC,90,2174 (1986) opls_106 15.03500 ; United-atom CH3 (CH3NH3+) JPC 90,2174 (1986) opls_107 15.03500 ; United-atom CH3 ((CH3)4N+) JPC 90,2174 (1986) opls_108 15.99940 ; United-atom Ether O JCC,11,958 (1990) opls_109 15.03500 ; United-atom Ether CH3 (-O) JCC,11,958 (1990) opls_110 14.02700 ; United-atom Ether CH2 (-O) JCC,11,958 (1990) opls_111 15.99940 ; O TIP3P Water opls_112 1.00800 ; H TIP3P Water opls_113 15.99940 ; O TIP4P Water opls_114 1.00800 ; H TIP4P Water opls_115 0.00000 ; M TIP4P Water opls_116 15.99940 ; O SPC Water opls_117 1.00800 ; H SPC Water opls_118 15.99940 ; O TIP5P Water opls_119 1.00800 ; H TIP5P Water opls_120 0.00000 ; L TIP5P Water opls_122 12.01100 ; C CCl4 opls_123 35.45300 ; Cl CCl4 opls_124 32.06000 ; S in UA DMSO opls_125 15.99940 ; O in UA DMSO opls_126 15.03500 ; CH3 in UA DMSO opls_127 14.00670 ; Updated ammonia parameters - JPC B 2001, 105, 6474 opls_128 1.00800 ; Updated ammonia parameters - JPC B 2001, 105, 6474 opls_129 20.17970 ; Neon Hirschfelder (Wiley,1954) opls_130 4.00260 ; Helium Hirschfelder (Wiley,1954) opls_131 12.01100 ; C in C=O for UA formamide, DMF. opls_132 15.03500 ; CH3 in HCON(CH3)2 DMF opls_135 12.01100 ; alkane CH3 opls_136 12.01100 ; alkane CH2 opls_137 12.01100 ; alkane CH opls_138 12.01100 ; alkane CH4 opls_139 12.01100 ; alkane C opls_140 1.00800 ; alkane H. opls_141 12.01100 ; alkene C (R2-C=) opls_142 12.01100 ; alkene C (RH-C=) opls_143 12.01100 ; alkene C (H2-C=) opls_144 1.00800 ; alkene H (H-C=) opls_145 12.01100 ; Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl opls_145B 12.01100 ; Biphenyl C1 opls_146 1.00800 ; Benzene H - 12 site. opls_147 12.01100 ; Naphthalene fusion C (C9) opls_148 12.01100 ; C: CH3, toluene opls_149 12.01100 ; C: CH2, ethyl benzene opls_150 12.01100 ; diene =CH-CH=; use #178 for =CR-CR= opls_151 35.45300 ; Cl in alkyl chlorides opls_152 12.01100 ; RCH2Cl in alkyl chlorides opls_153 1.00800 ; H in RCH2Cl in alkyl chlorides opls_154 15.99940 ; all-atom O: mono alcohols opls_155 1.00800 ; all-atom H(O): mono alcohols, OP(=O)2 opls_156 1.00800 ; all-atom H(C): methanol opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols opls_158 12.01100 ; all-atom C: CH, alcohols opls_159 12.01100 ; all-atom C: C, alcohols opls_160 12.01100 ; CH2 Trifluoroethanol opls_161 12.01100 ; CF3 Trifluoroethanol opls_162 15.99940 ; OH Trifluoroethanol opls_163 1.00800 ; HO Trifluoroethanol opls_164 18.99840 ; F Trifluoroethanol opls_165 1.00800 ; H Trifluoroethanol opls_166 12.01100 ; C(OH) phenol Use with all opls_167 15.99940 ; O phenol atom C, H 145 & 146 opls_168 1.00800 ; H phenol opls_169 15.99940 ; O: diols opls_170 1.00800 ; H(O): diols opls_171 15.99940 ; O: triols opls_172 1.00800 ; H(O): triols opls_173 12.01100 ; C(H2OH): triols opls_174 12.01100 ; C(HROH): triols opls_175 12.01100 ; C(R2OH): triols opls_176 1.00800 ; H(CXOH): triols opls_178 12.01100 ; diene =CR-CR=; use #150 for =CH-CH= opls_179 15.99940 ; O: anisole opls_180 15.99940 ; O: dialkyl ether opls_181 12.01100 ; C(H3OR): methyl ether opls_182 12.01100 ; C(H2OR): ethyl ether opls_183 12.01100 ; C(HOR): i-Pr ether, allose opls_184 12.01100 ; C(OR): t-Bu ether opls_185 1.00800 ; H(COR): alpha H ether opls_186 15.99940 ; O: acetal ether opls_187 15.99940 ; O(H): hemiacetal opls_188 1.00800 ; H(O): hemiacetal opls_189 12.01100 ; C(H2O2): acetal OCH2O opls_190 1.00800 ; H(CHO2): acetal OCH2O opls_191 12.01100 ; C(H2O2): hemiacetal OCH2OH opls_192 1.00800 ; H(CHO2): hemiacetal OCH2OH opls_193 12.01100 ; C(HCO2): acetal OCHRO opls_194 1.00800 ; H(CHO2): acetal OCHRO opls_195 12.01100 ; C(HCO2): hemiacetal OCHROH opls_196 1.00800 ; H(C2O2): hemiacetal OCHROH opls_197 12.01100 ; C(C2O2): acetal OCRRO opls_198 12.01100 ; C(C2O2): hemiacetal OCRROH opls_199 12.01100 ; C(O,Me): anisole opls_200 32.06000 ; all-atom S: thiols opls_201 32.06000 ; S IN H2S JPC,90,6379 (1986) opls_202 32.06000 ; all-atom S: sulfides, S=C opls_203 32.06000 ; all-atom S: disulfides opls_204 1.00800 ; all-atom H(S): thiols opls_205 1.00800 ; H IN H2S JPC,90,6379 (1986) opls_206 12.01100 ; all-atom C: CH2, thiols opls_207 12.01100 ; all-atom C: CH, thiols opls_208 12.01100 ; all-atom C: C, thiols opls_209 12.01100 ; all-atom C: CH3, sulfides opls_210 12.01100 ; all-atom C: CH2, sulfides opls_211 12.01100 ; all-atom C: CH, sulfides opls_212 12.01100 ; all-atom C: C, sulfides opls_213 12.01100 ; all-atom C: CH3, disulfides opls_214 12.01100 ; all-atom C: CH2, disulfides opls_215 12.01100 ; all-atom C: CH, disulfides opls_216 12.01100 ; all-atom C: C, disulfides opls_217 12.01100 ; all-atom C: CH3, methanethiol opls_218 12.01100 ; C in CH2OH - benzyl alcohols opls_219 12.01100 ; C in CHROH - benzyl alcohols opls_220 12.01100 ; C in CR2OH - benzyl alcohols opls_221 12.01100 ; C(CH2OH) - benzyl alcohols opls_222 32.06000 ; S in thioanisoles opls_223 12.01100 ; C in RCH2NH2. Use #223B for AA Calpha. opls_223B 12.01100 ; Gly Calpha opls_224 12.01100 ; C in R2CHNH2. Use #224B for AA Calpha. opls_224B 12.01100 ; Calpha in most AA (except Gly,Pro,Aib) opls_225 12.01100 ; C in R3CNH2. Use #225B for AA Calpha. opls_225B 12.01100 ; Aib Calpha. opls_226 35.45300 ; chloroalkene Cl (ClH-C=) - see also #398 opls_227 12.01100 ; chloroalkene C (ClH-C=) opls_228 12.01100 ; C(SMe) thioanisole opls_229 12.01100 ; C on N: secondary N-CHR2 amide opls_230 12.01100 ; C on N: secondary N-CR3 amide opls_231 12.01100 ; C: C=O in benzophenone opls_232 12.01100 ; C: C=O in benzaldehyde,acetophenone (CH) opls_233 12.01100 ; C: C=O in acetophenone (CMe) opls_234 12.01100 ; C: C=O in benzamide opls_235 12.01100 ; C=O in amide, dmf, peptide bond opls_236 15.99940 ; O: C=O in amide. Acyl R on C in amide is neutral - opls_237 14.00670 ; N: primary amide. use alkane parameters. opls_238 14.00670 ; N: secondary amide, peptide bond (see #279 for formyl H) opls_239 14.00670 ; N: tertiary amide opls_240 1.00800 ; H on N: primary amide opls_241 1.00800 ; H on N: secondary amide opls_242 12.01100 ; C on N: secondary N-Me amide opls_243 12.01100 ; C on N: tertiary N-Me amide opls_244 12.01100 ; C on N: secondary N-CH2R amide opls_245 12.01100 ; C on N: tertiary N-CH2R amide, Pro CD opls_246 12.01100 ; C on N: tertiary N-CHR2 amide, Pro CA opls_247 12.01100 ; C in O=C(NH2)2 Urea opls_248 15.99940 ; O in O=C(NH2)2 Urea Isr. J. Chem opls_249 14.00670 ; N in O=C(NH2)2 Urea 33, 323 (93) opls_250 1.00800 ; H in O=C(NH2)2 Urea opls_251 14.00670 ; N in imide opls_252 12.01100 ; C(=O) in imide opls_253 15.99940 ; O in imide opls_254 1.00800 ; H(N) in imide opls_255 1.00800 ; H(C) in formimide opls_256 12.01100 ; C in CH3 imide opls_257 12.01100 ; C in RCH2 imide opls_258 12.01100 ; C in R2CH imide opls_259 12.01100 ; C in R3C imide opls_260 12.01100 ; C(CN) benzonitrile opls_261 12.01100 ; C(N) benzonitrile opls_262 14.00670 ; N benzonitrile opls_263 12.01100 ; C(Cl) chlorobenzene opls_264 35.45300 ; Cl chlorobenzene opls_265 14.00670 ; N: N-phenylacetamide opls_266 12.01100 ; ipso C in N-phenylacetamide opls_267 12.01100 ; Co in CCOOH carboxylic acid opls_268 15.99940 ; Oh in CCOOH R in RCOOH is opls_269 15.99940 ; Oc in CCOOH neutral; use #135-#140 opls_270 1.00800 ; H in CCOOH opls_271 12.01100 ; C in COO- carboxylate opls_272 15.99940 ; O: O in COO- carboxylate,peptide terminus opls_273 12.01100 ; C: CH3, carboxylate ion opls_274 12.01100 ; C: CH2, carboxylate ion opls_275 12.01100 ; C: CH, carboxylate ion opls_276 12.01100 ; C: C, carboxylate ion opls_277 12.01100 ; AA C: aldehyde - for C-alpha use #135-#139 opls_278 15.99940 ; AA O: aldehyde opls_279 1.00800 ; AA H-alpha in aldehyde & formamide opls_280 12.01100 ; AA C: ketone - for C-alpha use #135-#139 opls_281 15.99940 ; AA O: ketone opls_282 1.00800 ; AA H on C-alpha in ketone & aldehyde opls_283 12.01100 ; CA on C-terminal ALA,CYS,SER,THR,HIS,ASP,ASN opls_284 12.01100 ; CA on C-terminal GLY opls_285 12.01100 ; CA on C-terminal PRO opls_286 14.00670 ; N (NH4+) JPC,90,2174 (1986) opls_287 14.00670 ; N (RNH3+) JPC,90,2174 (1986) opls_288 14.00670 ; N (R4N+) JPC,90,2174 (1986) opls_289 1.00800 ; H (NH4+) JPC,90,2174 (1986) opls_290 1.00800 ; H (RNH3+) JPC,90,2174 (1986) opls_291 12.01100 ; C in CH3NH3+ opls_292 12.01100 ; C in RCH2NH3+ opls_292B 12.01100 ; CA in GLY-NH3+ N-term. opls_293 12.01100 ; C in R2CHNH3+ opls_293B 12.01100 ; CA in NH3+ N-term, All AA except GLY & PRO opls_294 12.01100 ; C in R3CNH3+ opls_295 12.01100 ; AA C-alpha on N-term PRO opls_296 12.01100 ; AA:C-delta in N-term PRO NH2+ opls_297 12.01100 ; CT in CH3NH2+R opls_298 12.01100 ; AA C-alpha in Gly zwitterion opls_299 12.01100 ; AA C-alpha in Ala zwitterion opls_300 14.00670 ; N: guanidinium NH2 opls_301 1.00800 ; H: guanidinium NH2 opls_302 12.01100 ; C: guanidinium C+ opls_303 14.00670 ; N: guanidinium NHR opls_304 1.00800 ; H: guanidinium NHR opls_305 12.01100 ; C: CH3, methylguanidinium opls_306 12.01100 ; C: CH3, ethylguanidinium opls_307 12.01100 ; C: CH2(D), ARG, ethylguanidinium opls_308 12.01100 ; C: CH2(G), ARG opls_309 14.00670 ; N (R2NH2+), N-terminal PRO NH2+ opls_310 1.00800 ; H (R2NH2+) opls_311 14.00670 ; DAP N1 (Diaminopyridine) opls_312 12.01100 ; DAP C2 opls_313 14.00670 ; DAP N-amine opls_314 1.00800 ; DAP H-amine opls_315 12.01100 ; DAP C3 opls_316 1.00800 ; DAP H3 opls_317 12.01100 ; DAP C4 opls_318 1.00800 ; DAP H4 opls_319 14.00670 ; Uracil & Thymine N1 - use #319B for nucleoside opls_319B 14.00670 ; Uracil & Thymine N1 - only for nucleoside opls_320 12.01100 ; Uracil & Thymine C2 opls_321 14.00670 ; Uracil & Thymine N3 opls_322 12.01100 ; Uracil & Thymine C4 opls_323 12.01100 ; Uracil & Thymine C5 opls_324 12.01100 ; Uracil & Thymine C6 opls_325 1.00800 ; Uracil & Thymine H-N1 opls_326 15.99940 ; Uracil O-C2 opls_327 1.00800 ; Uracil H-N3 opls_328 15.99940 ; Uracil O-C4 opls_329 1.00800 ; Uracil H-C5 opls_330 1.00800 ; Uracil H-C6 opls_331 12.01100 ; Thymine C-C5 opls_332 1.00800 ; Thymine H-CC5 opls_333 14.00670 ; Cytosine N1 -use #333B for nucleoside opls_333B 14.00670 ; Cytosine N1 - for nucleoside opls_334 12.01100 ; Cytosine C2 opls_335 14.00670 ; Cytosine N3 opls_336 12.01100 ; Cytosine C4 Nucleotide base opls_337 12.01100 ; Cytosine C5 parameters: opls_338 12.01100 ; Cytosine C6 JACS,113,2810(1991) opls_339 1.00800 ; Cytosine H-N1 opls_340 15.99940 ; Cytosine O-C2 opls_341 14.00670 ; Cytosine N-C4 opls_342 1.00800 ; Cytosine H-NC4/N3 opls_343 1.00800 ; Cytosine H-NC4/C5 opls_344 1.00800 ; Cytosine H-C5 opls_345 1.00800 ; Cytosine H-C6 opls_346 14.00670 ; Adenine N1 opls_347 12.01100 ; Adenine C2 opls_348 14.00670 ; Adenine N3 opls_349 12.01100 ; Adenine C4 opls_350 12.01100 ; Adenine C5 opls_351 12.01100 ; Adenine C6 opls_352 14.00670 ; Adenine & Guanine N7 opls_353 12.01100 ; Adenine & Guanine C8 opls_354 14.00670 ; Adenine & Guanine N9 - use #354B for nucleoside opls_354B 14.00670 ; Adenine & Guanine N9 - nucleoside only opls_355 1.00800 ; Adenine & Guanine H-C2 opls_356 14.00670 ; Adenine & Guanine N-C6 opls_357 1.00800 ; Adenine & Guanine H-NC6/N1 opls_358 1.00800 ; Adenine & Guanine H-NC6/C5 opls_359 1.00800 ; Adenine & Guanine H-C8 Guanine opls_360 1.00800 ; Adenine & Guanine H-N9 Guanine opls_361 14.00670 ; Guanine N1 opls_362 12.01100 ; Guanine C2 opls_363 14.00670 ; Guanine N3 opls_364 12.01100 ; Guanine C4 opls_365 12.01100 ; Guanine C5 opls_366 12.01100 ; Guanine C6 opls_367 1.00800 ; Guanine H-N1 opls_368 14.00670 ; Guanine N-C2 opls_369 1.00800 ; Guanine H-NC2 opls_370 15.99940 ; Guanine O-C6 opls_371 12.01100 ; 9-Me Adenine or Guanine C-N9 opls_372 1.00800 ; 9-Me Adenine or Guanine H-CN9 opls_373 12.01100 ; 1-Me Uracil or Thymine C-N1 opls_374 1.00800 ; 1-Me Uracil or Thymine H-CN1 opls_375 12.01100 ; 1-Me Cytosine C-N1 opls_376 1.00800 ; 1-Me Cytosine H-CN1 opls_377 14.00670 ; CytH+ N1 Use #377B for nucleoside. opls_377B 14.00670 ; CytH+ N1 - nucleoside only opls_378 12.01100 ; CytH+ C2 opls_379 14.00670 ; CytH+ N3 Protonated cytosine. opls_380 12.01100 ; CytH+ C4 opls_381 12.01100 ; CytH+ C5 opls_382 12.01100 ; CytH+ C6 opls_383 1.00800 ; CytH+ H-N1 opls_384 15.99940 ; CytH+ O-C2 opls_385 1.00800 ; CytH+ H-N3 opls_386 14.00670 ; CytH+ N-C4 opls_387 1.00800 ; CytH+ H-NC4/N3 opls_388 1.00800 ; CytH+ H-NC4/C5 opls_389 1.00800 ; CytH+ H-C5 opls_390 1.00800 ; CytH+ H-C6 opls_391 12.01100 ; 1-Me CytH+ C-N1 opls_392 1.00800 ; 1-Me CytH+ H-CN1 opls_393 30.97376 ; P dimethylphosphate anion UA - see #440 for AA opls_394 15.99940 ; O(=) dimethylphosphate anion UA - see #440 for AA opls_395 15.99940 ; O(-) dimethylphosphate anion UA - see #440 for AA opls_396 12.01100 ; C in CH3 dimethylphosphate anion UA - see #440 for AA opls_400 18.99840 ; F- JACS 106, 903 (1984) opls_401 35.45300 ; Cl- JACS 106, 903 (1984) opls_402 79.90400 ; Br- JACS 107, 7793(1985) opls_403 126.90450 ; I- JACS 120, 5104(1998) opls_404 6.94100 ; Li+ JACS 106, 903 (1984) opls_405 22.98977 ; Na+ JACS 106, 903 (1984) opls_406 6.94100 ; Li+ opls_407 22.98977 ; Na+ Aqvists cation opls_408 39.09830 ; K+ parameters: opls_409 85.46780 ; Rb+ JPC,94, 8021 (90) opls_410 132.90540 ; Cs+ opls_411 24.30500 ; Mg++ opls_412 40.08000 ; Ca++ opls_413 87.62000 ; Sr++ opls_414 137.33000 ; Ba++ opls_415 12.01100 ; C in CH3S- thiolate opls_416 1.00800 ; H in CH3S- opls_417 32.06000 ; S in CH3S- opls_418 12.01100 ; C in CH3O- alkoxide opls_419 1.00800 ; H in CH3O- opls_420 15.99940 ; O in CH3O- opls_421 12.01100 ; C1 in CH2CN- RCN- opls_422 1.00800 ; H in CH2CN- opls_423 12.01100 ; C2 in CH2CN- JACS 111,4190 (89) opls_424 14.00670 ; N in CH2CN- opls_425 12.01100 ; C in CH3NH- opls_426 1.00800 ; HC in CH3NH- RNH- opls_427 14.00670 ; N in CH3NH- opls_428 1.00800 ; HN in CH3NH- opls_429 12.01100 ; C2 in CH3CH2- RCH2- opls_430 1.00800 ; H in CH3CH2- opls_431 12.01100 ; C1 in CH3CH2- opls_432 1.00800 ; H1 in CH3CH2- opls_433 0.00000 ; LP in CH3CH2- opls_434 15.99940 ; O in OH- Hyroxide O-H = 0.953 A opls_435 1.00800 ; H in OH- JACS 108, 2517 (86) opls_436 0.00000 ; U in UO2+ J Mol Struct 366, 55 (96) opls_437 15.99940 ; O in UO2+ r(U-O) = 1.80 A opls_440 30.97376 ; P in Me2PO4-, Me2PO4H opls_441 15.99940 ; O= in Me2PO4-, Me2PO4H opls_442 15.99940 ; OMe in Me2PO4-, Me2PO4H dimethylphosphate opls_443 12.01100 ; C in Me2PO4-, Me2PO4H dimetylphosphate opls_444 1.00800 ; H in Me2PO4-, Me2PO4H 6-31+G* CHELPG opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2 opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2 opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2 opls_450 30.97376 ; P in MePO3Me-, MePO3HMe opls_451 15.99940 ; O= in MePO3Me-, MePO3HMe opls_452 15.99940 ; OMe in MePO3Me-, MePO3HMe methyl opls_453 12.01100 ; C(O) MePO3Me-, MePO3HMe methylphosphonate opls_454 1.00800 ; H(CO) MePO3Me-, MePO3HMe 6-31+G* CHELPG opls_455 12.01100 ; C(P) MePO3Me-, MePO3HMe opls_456 1.00800 ; H(CP) MePO3Me-, MePO3HMe opls_457 12.01100 ; Cipso benzyl methylphosphonate opls_458 12.01100 ; C(O) benzyl methylphosphonate opls_459 1.00800 ; H(CO) benzyl methylphosphonate opls_460 12.01100 ; Cipso methyl benzylphosphonate opls_461 12.01100 ; C(P) methyl benzylphosphonate opls_462 1.00800 ; H(CP) methyl benzylphosphonate opls_463 12.01100 ; Cipso C6H5OPO3(2-) use with #445-#447 opls_465 12.01100 ; AA C: esters - for R on C=O, use #280-#282 opls_466 15.99940 ; AA =O: esters opls_467 15.99940 ; AA -OR: ester opls_468 12.01100 ; methoxy C in esters - see also #490-#492 opls_469 1.00800 ; methoxy Hs in esters opls_470 12.01100 ; Co in benzoic acid opls_471 12.01100 ; Co in methyl benzoate, aryl ester opls_472 12.01100 ; Cipso phenyl ester opls_473 15.99940 ; AA -OR phenyl ester opls_474 32.06000 ; S in sulfonamide, S(=O)2(OR) opls_475 15.99940 ; O in sulfonamide, S(=O)2(OR) opls_476 12.01100 ; CH3 attached to S of sulfonamide opls_477 1.00800 ; H of Me attached to S of sulfonamide opls_478 14.00670 ; N: primary amide of sulfonamide opls_479 1.00800 ; H on N: primary sulfonamide opls_480 14.00670 ; N secondary amide of sulfonamide opls_481 1.00800 ; H on N: secondary sulfonamide opls_482 12.01100 ; alpha CH3-N of sulfonamide opls_483 1.00800 ; H of alpha CH3-N of sulfonamide opls_484 12.01100 ; alpha CH2-N of sulfonamide. Use q=0.45 for CRH-N, q=0.65 for O=N-C-CH-N. opls_485 1.00800 ; H of alpha CH2-N of sulfonamide opls_486 12.01100 ; beta CH3 of N-ethyl sulfonamide opls_487 1.00800 ; H of beta CH3 of N-ethyl sulfonamide opls_488 12.01100 ; benzene C attached to S of sulfonamide opls_490 12.01100 ; C(H2OS) ethyl ester opls_491 12.01100 ; C(HOS) i-pr ester opls_492 12.01100 ; C(OS) t-bu ester opls_493 32.06000 ; S in sulfone opls_494 15.99940 ; O in sulfone opls_496 32.06000 ; sulfoxide - all atom opls_497 15.99940 ; sulfoxide - all atom opls_498 12.01100 ; CH3 all-atom C: sulfoxide opls_499 12.01100 ; CH2 all-atom C: sulfoxide opls_500 12.01100 ; CG in Trp opls_501 12.01100 ; CD C in Trp opls_502 12.01100 ; CE C in Trp opls_503 14.00670 ; NE in Trp opls_504 1.00800 ; H on NE in Trp opls_505 12.01100 ; CB in His opls_506 12.01100 ; CE1 in HID, HIE opls_507 12.01100 ; CD2 in HID, CG in HIE opls_508 12.01100 ; CG in HID, CD2 in HIE opls_509 12.01100 ; CE1 in HIP opls_510 12.01100 ; CG, CD2 in HIP opls_511 14.00670 ; NE in HID, ND in HIE opls_512 14.00670 ; N in HIP opls_513 1.00800 ; H on N in HIP opls_514 12.01100 ; CD1 in TRP opls_515 12.01100 ; all-atom C: CH, isopropyl benzene opls_516 12.01100 ; all-atom C: C, t-butyl benzene opls_517 12.01100 ; vinyl ether HCOR opls_518 12.01100 ; vinyl ether RCOR opls_520 14.00670 ; N in pyridine 6-31G* opls_521 12.01100 ; C1 in pyridine CHELPG opls_522 12.01100 ; C2 in pyridine charges opls_523 12.01100 ; C3 in pyridine for opls_524 1.00800 ; H1 in pyridine 520-619 opls_525 1.00800 ; H2 in pyridine opls_526 1.00800 ; H3 in pyridine opls_527 14.00670 ; N in pyrazine opls_528 12.01100 ; C in pyrazine opls_529 1.00800 ; H in pyrazine opls_530 14.00670 ; N in pyrimidine opls_531 12.01100 ; C2 in pyrimidine opls_532 12.01100 ; C4 in pyrimidine opls_533 12.01100 ; C5 in pyrimidine opls_534 1.00800 ; H2 in pyrimidine opls_535 1.00800 ; H4 in pyrimidine opls_536 1.00800 ; H5 in pyrimidine opls_537 14.00670 ; N in pyridazine opls_538 12.01100 ; C3 in pyridazine opls_539 12.01100 ; C4 in pyridazine opls_540 1.00800 ; H3 in pyridazine opls_541 1.00800 ; H4 in pyridazine opls_542 14.00670 ; N in pyrrole opls_543 12.01100 ; C2 in pyrrole opls_544 12.01100 ; C3 in pyrrole opls_545 1.00800 ; H1 in pyrrole opls_546 1.00800 ; H2 in pyrrole opls_547 1.00800 ; H3 in pyrrole opls_548 14.00670 ; N1 in pyrazole opls_549 14.00670 ; N2 in pyrazole opls_550 12.01100 ; C3 in pyrazole opls_551 12.01100 ; C4 in pyrazole opls_552 12.01100 ; C5 in pyrazole opls_553 1.00800 ; H1 in pyrazole opls_554 1.00800 ; H3 in pyrazole opls_555 1.00800 ; H4 in pyrazole opls_556 1.00800 ; H5 in pyrazole opls_557 14.00670 ; N1 in imidazole opls_558 12.01100 ; C2 in imidazole opls_559 14.00670 ; N3 in imidazole opls_560 12.01100 ; C4 in imidazole opls_561 12.01100 ; C5 in imidazole opls_562 1.00800 ; H1 in imidazole opls_563 1.00800 ; H2 in imidazole opls_564 1.00800 ; H4 in imidazole opls_565 1.00800 ; H5 in imidazole opls_566 15.99940 ; O in furan opls_567 12.01100 ; C2 in furan opls_568 12.01100 ; C3 in furan opls_569 1.00800 ; H2 in furan opls_570 1.00800 ; H3 in furan opls_571 15.99940 ; O in oxazole opls_572 12.01100 ; C2 in oxazole opls_573 14.00670 ; N in oxazole opls_574 12.01100 ; C4 in oxazole opls_575 12.01100 ; C5 in oxazole opls_576 1.00800 ; H2 in oxazole opls_577 1.00800 ; H4 in oxazole opls_578 1.00800 ; H5 in oxazole opls_579 15.99940 ; O in isoxazole opls_580 14.00670 ; N in isoxazole opls_581 12.01100 ; C3 in isoxazole opls_582 12.01100 ; C4 in isoxazole opls_583 12.01100 ; C5 in isoxazole opls_584 1.00800 ; H3 in isoxazole opls_585 1.00800 ; H4 in isoxazole opls_586 1.00800 ; H5 in isoxazole opls_587 14.00670 ; N1 in indole opls_588 12.01100 ; C2 in indole opls_589 12.01100 ; C3 in indole opls_590 12.01100 ; C4 in indole opls_591 12.01100 ; C5 in indole opls_592 12.01100 ; C6 in indole opls_593 12.01100 ; C7 in indole opls_594 12.01100 ; C8 in indole opls_595 12.01100 ; C9 in indole opls_596 1.00800 ; H1 in indole opls_597 1.00800 ; H2 in indole opls_598 1.00800 ; H3 in indole opls_599 1.00800 ; H4 in indole opls_600 1.00800 ; H5 in indole opls_601 1.00800 ; H6 in indole opls_602 1.00800 ; H7 in indole opls_603 14.00670 ; N1 in quinoline opls_604 12.01100 ; C2 in quinoline opls_605 12.01100 ; C3 in quinoline opls_606 12.01100 ; C4 in quinoline opls_607 12.01100 ; C5 in quinoline opls_608 12.01100 ; C6 in quinoline opls_609 12.01100 ; C7 in quinoline opls_610 12.01100 ; C8 in quinoline opls_611 12.01100 ; C9 in quinoline opls_612 12.01100 ; C10 in quinoline opls_613 1.00800 ; H2 in quinoline opls_614 1.00800 ; H3 in quinoline opls_615 1.00800 ; H4 in quinoline opls_616 1.00800 ; H5 in quinoline opls_617 1.00800 ; H6 in quinoline opls_618 1.00800 ; H7 in quinoline opls_619 1.00800 ; H8 in quinoline opls_620 14.00670 ; N1 in purine opls_621 12.01100 ; C2 in purine opls_622 14.00670 ; N3 in purine opls_623 12.01100 ; C4 in purine opls_624 12.01100 ; C5 in purine opls_625 12.01100 ; C6 in purine opls_626 14.00670 ; N7 in purine opls_627 12.01100 ; C8 in purine opls_628 14.00670 ; N9 in purine opls_629 1.00800 ; H2 in purine opls_630 1.00800 ; H6 in purine opls_631 1.00800 ; H8 in purine opls_632 1.00800 ; H9 in purine opls_633 32.06000 ; S in thiazole opls_634 12.01100 ; C2 in thiazole opls_635 14.00670 ; N in thiazole opls_636 12.01100 ; C4 in thiazole opls_637 12.01100 ; C5 in thiazole opls_638 1.00800 ; H2 in thiazole opls_639 1.00800 ; H4 in thiazole opls_640 1.00800 ; H5 in thiazole opls_641 14.00670 ; N in 1,3,5-triazine opls_642 12.01100 ; C in 1,3,5-triazine opls_643 1.00800 ; H in 1,3,5-triazine opls_644 12.01100 ; C5 in serotonin opls_645 12.01100 ; C on C3 in serotonin opls_646 14.00670 ; N1,N10 in 1,10-phenanthroline opls_647 12.01100 ; C2,C9 in 1,10-phenanthroline opls_648 12.01100 ; C3,C8 in 1,10-phenanthroline opls_649 12.01100 ; C4,C7 in 1,10-phenanthroline opls_650 12.01100 ; C12,C14 in 1,10-phenanthroline opls_651 12.01100 ; C11,C13 in 1,10-phenanthroline opls_652 12.01100 ; C5 in 1,10-phenanthroline opls_653 1.00800 ; H2,H9 in 1,10-phenanthroline opls_654 1.00800 ; H3,H8 in 1,10-phenanthroline opls_655 1.00800 ; H4,H7 in 1,10-phenanthroline opls_656 1.00800 ; H5,H6 in 1,10-phenanthroline opls_670 12.01100 ; CH3, 2-methyl pyridine opls_671 12.01100 ; CH2, 2-ethyl pyridine opls_672 12.01100 ; CH3, 3-methyl pyridazine opls_673 12.01100 ; CH2, 3-ethyl pyridazine opls_674 12.01100 ; CH3, 4-methyl pyrimidine opls_675 12.01100 ; CH2, 4-ethyl pyrimidine opls_676 12.01100 ; CH3, 2-methyl pyrazine opls_677 12.01100 ; CH2, 2-ethyl pyrazine opls_678 12.01100 ; CH3, 2-methyl pyrrole opls_679 12.01100 ; CH2, 2-ethyl pyrrole opls_680 12.01100 ; CH3, 2-methyl furan opls_681 12.01100 ; CH2, 2-ethyl furan opls_697 0.00000 ; Ac+3 Actinide params - opls_698 0.00000 ; Th+4 opls_699 0.00000 ; Am+3 F. van Veggel opls_700 12.01100 ; C+ in t-butyl+ B3LYP/6-31G* opls_701 12.01100 ; C in t-butyl+ charges opls_702 1.00800 ; H in t-butyl+ opls_703 0.00000 ; La+3 opls_704 0.00000 ; Nd+3 Lanthanide params - opls_705 0.00000 ; Eu+3 F. van Veggel, Chem Eur J 5, 90 (1999). opls_706 0.00000 ; Gd+3 opls_707 0.00000 ; Yb+3 see also JPC-A 104, 7659 (2000) opls_708 12.01100 ; C in Cl..CH3..Cl- TS opls_709 35.45300 ; Cl charges: JACS 117,2024 (95) opls_710 1.00800 ; H in Cl..CH3..Cl- TS opls_711 12.01100 ; CH2 C: cyclopropane opls_712 12.01100 ; CHR C: cyclopropane opls_713 12.01100 ; CR2 C: cyclopropane opls_714 12.01100 ; C in C5H5- cyclopentadienyl anion opls_715 1.00800 ; H in C5H5- cyclopentadienyl anion opls_716 12.01100 ; C in C5H5 cyclopentadienyl radical opls_717 1.00800 ; H in C5H5 cyclopentadienyl radical opls_718 12.01100 ; C(F) fluorobenzene opls_719 18.99840 ; F fluorobenzene opls_720 12.01100 ; C(F) hexafluorobenzene opls_721 18.99840 ; F hexafluorobenzene opls_722 79.90400 ; Br alkyl bromide (UA, but probably ok for AA) opls_724 12.01100 ; C(CF3) trifluoromethylbenzene opls_725 12.01100 ; CF3 trifluoromethylbenzene opls_726 18.99840 ; F trifluoromethylbenzene opls_727 12.01100 ; C(F) difluorobenzenes opls_728 18.99840 ; F difluorobenzenes opls_729 12.01100 ; C(Br) bromobenzene opls_730 79.90400 ; Br bromobenzene opls_731 12.01100 ; C(I) iodobenzene - tentative opls_732 126.90450 ; I iodobenzene - tentative opls_733 12.01100 ; all-atom C: CH, cyclopropyl benzene opls_734 32.06000 ; all-atom S: thiophenol (HS is #204) opls_735 12.01100 ; C(S) thiophenol opls_736 12.01100 ; CG of Benzamidine opls_737 12.01100 ; CD of Benzamidine opls_738 12.01100 ; CE of Benzamidine opls_739 12.01100 ; CZ of Benzamidine opls_740 1.00800 ; HD of Benzamidine opls_741 1.00800 ; HE of Benzamidine opls_742 12.01100 ; C+ of Benzamidine opls_743 14.00670 ; N-H2 of Benzamidine opls_744 1.00800 ; H1-N of Benzamidine opls_745 1.00800 ; H2-N of Benzamidine opls_746 1.00800 ; H-CG of Benzamidine opls_747 12.01100 ; CH3 in neutral MeGDN opls_748 12.01100 ; CD of neutral ARG opls_749 14.00670 ; NE of neutral ARG opls_750 14.00670 ; N1 of neutral ARG (HN=CZ) opls_751 14.00670 ; N2 of neutral ARG (H2N-CZ) opls_752 12.01100 ; CZ of neutral ARG opls_753 14.00670 ; N IN RCN nitriles opls_754 12.01100 ; C IN RCN nitriles opls_755 12.01100 ; C of CH3 in CH3CN opls_756 12.01100 ; C of CH2 in RCH2CN opls_757 12.01100 ; C of CH in R2CHCN opls_758 12.01100 ; C of C in R3CCN opls_759 1.00800 ; HC-CT-CN alpha-H in nitriles opls_760 14.00670 ; N in nitro R-NO2 opls_761 15.99940 ; O in nitro R-NO2 opls_762 12.01100 ; CT-NO2 nitromethane opls_763 1.00800 ; HC-CT-NO2 alpha-H in nitroalkanes opls_764 12.01100 ; CT-NO2 nitroethane opls_765 12.01100 ; CT-NO2 2-nitropropane opls_766 12.01100 ; CT-NO2 2-methyl-2-nitropropane opls_767 14.00670 ; N in nitro Ar-NO2 opls_768 12.01100 ; C(NO2) nitrobenzene opls_771 15.99940 ; propylene carbonate O (Luciennes param.) opls_772 12.01100 ; propylene carbonate C=O opls_773 15.99940 ; propylene carbonate OS opls_774 12.01100 ; propylene carbonate C in CH2 opls_775 12.01100 ; propylene carbonate C in CH opls_776 12.01100 ; propylene carbonate C in CH3 opls_777 1.00800 ; propylene carbonate H in CH2 opls_778 1.00800 ; propylene carbonate H in CH opls_779 1.00800 ; propylene carbonate H in CH3 opls_781 30.97376 ; phosphonium R4P+ opls_782 12.01100 ; CH3PR3+ 6-31G* CHELPG opls_783 12.01100 ; RCH2PR3+ opls_784 1.00800 ; H in CH3PR3+ opls_785 30.97376 ; P in PF6- opls_786 18.99840 ; F in PF6- opls_787 14.00670 ; N in NO3- opls_788 15.99940 ; O in NO3- opls_795 15.99940 ; O TIP4F Water opls_796 1.00800 ; H TIP4F Water opls_797 0.00000 ; M TIP4F Water opls_900 14.00670 ; N primary amines opls_901 14.00670 ; N secondary amines, aziridine N1 opls_902 14.00670 ; N tertiary amines opls_903 12.01100 ; CH3(N) primary aliphatic amines, H(C) is #911 opls_904 12.01100 ; CH3(N) secondary aliphatic amines, H(C) is #911 opls_905 12.01100 ; CH3(N) tertiary aliphatic amines, H(C) is #911 opls_906 12.01100 ; CH2(N) primary aliphatic amines, H(C) is #911 opls_906B 12.01100 ; CA in GLY-NH2 N-terminus opls_907 12.01100 ; CH2(N) secondary aliphatic amines, aziridine C2,C3H opls_908 12.01100 ; CH2(N) tertiary aliphatic amines, H(C) is #911 opls_909 1.00800 ; H(N) primary amines opls_910 1.00800 ; H(N) secondary amines opls_911 1.00800 ; H(C) for C bonded to N in amines, diamines (aziridine H2,H3) opls_912 12.01100 ; CH primary isopropyl amine opls_912B 12.01100 ; CA in NH2 N-terminus. All AA except GLY, PRO opls_913 12.01100 ; C primary t-butyl amine opls_914 12.01100 ; CH secondary isopropyl amine opls_915 12.01100 ; CH tertiary isopropyl amine opls_916 12.01100 ; C(NH2) aniline opls_917 12.01100 ; C(NH2) N-methylaniline opls_918 12.01100 ; C(NH2) N,N-dimethylaniline opls_925 12.01100 ; alkyne RC%CH terminal C acetylene opls_926 1.00800 ; alkyne RC%CH terminal H opls_927 12.01100 ; alkyne RC%CH C2 R-with 2 or 3 H opls_928 12.01100 ; alkyne RC%CH C2 R-with 1 H opls_929 12.01100 ; alkyne RC%CH C2 R-with no H or R=Phenyl opls_930 1.00800 ; alkyne RC%CH H on C3 (for C3 use #135-#139) opls_931 12.01100 ; alkyne RC%CR opls_940 14.00670 ; N (R3NH+) opls_941 1.00800 ; H (R3NH+) opls_942 12.01100 ; C in CH3NHR2+ opls_943 12.01100 ; C in RCH2NHR2+ opls_944 12.01100 ; C in R2CHNHR2+ opls_945 12.01100 ; C in R3CNHR2+ opls_950 1.00800 ; glycine zwit. 6-31G* CHELPG charges opls_951 12.01100 ; glycine zwit. 6-31G* CHELPG charges opls_952 12.01100 ; glycine zwit. 6-31G* CHELPG charges opls_953 14.00670 ; glycine zwit. 6-31G* CHELPG charges opls_954 15.99940 ; glycine zwit. 6-31G* CHELPG charges opls_955 1.00800 ; glycine zwit. 6-31G* CHELPG charges opls_956 18.99840 ; F in monoalkyl fluorides (tentative) opls_957 12.01100 ; RCH2F in monoalkyl fluorides (tentative) opls_958 1.00800 ; H in RCHF in monoalkyl fluorides (tentative) opls_959 12.01100 ; R2CHF in monoalkyl fluorides (tentative) opls_960 12.01100 ; R3CF in monoalkyl fluorides (tentative) opls_961 12.01100 ; CF3 perfluoroalkanes opls_962 12.01100 ; CF2 perfluoroalkanes opls_963 12.01100 ; CF perfluoroalkanes opls_964 12.01100 ; CF4 opls_965 18.99840 ; F: perfluoroalkanes MNH3 0.0 ; Dummy mass in rigid tetraedrical NH3 group MNH2 0.0 ; Dummy mass in rigid umbrella-shaped NH2 group MCH3A 0.0 ; Dummy mass in rigid tetraedrical CH3 group MCH3B 0.0 ; Dummy mass in rigid tetraedrical CH3 group MW 0.0 ; Dummy mass in rigid tyrosine rings DUM 0.0 ; Dummy mass in TIP4P etc. ; These ion atomtypes are NOT part of OPLS, but since they are ; needed for some proteins we have added them. Cu2+ 63.546 ; Copper. See Inorg. Chem. 40, 5223 (2001). Fe2+ 55.847 ; Iron Zn2+ 65.370 ; Zinc Ar 39.948 ; Argon ; Added by DvdS 05/2005 copied from GROMACS force field. SI 28.080 ; Silicium in Glass etc. ; Some esoteric OPLS atomtypes are not freely available (or depreciated). ; Interaction types involving these have been commented out. [ bondtypes ] ; i j func b0 kb OW HW 1 0.09572 502080.0 ; For TIP4F Water - wlj 1/98 OW LP 1 0.01750 753120.0 ; -idem- C* HC 1 0.10800 284512.0 ; C C3 1 0.15220 265265.6 ; END C_2 C3 1 0.15220 265265.6 ; END C_3 C3 1 0.15220 265265.6 ; END C CA 1 0.14900 334720.0 ; wlj 8/97 C_2 CA 1 0.14900 334720.0 ; wlj 8/97 C_3 CA 1 0.14900 334720.0 ; wlj 8/97 C CB 1 0.14190 374049.6 ; GUA C_2 CB 1 0.14190 374049.6 ; GUA C_3 CB 1 0.14190 374049.6 ; GUA C CM 1 0.14440 343088.0 ; THY C_2 CM 1 0.14440 343088.0 ; THY C_3 CM 1 0.14440 343088.0 ; THY C CS 1 0.14900 334720.0 ; C_2 CS 1 0.14900 334720.0 ; C_3 CS 1 0.14900 334720.0 ; C CT 1 0.15220 265265.6 ; C_2 CT 1 0.15220 265265.6 ; C_3 CT 1 0.15220 265265.6 ; C CT_2 1 0.15220 265265.6 ; AA Calpha C_3 CT_2 1 0.15220 265265.6 ; AA C-term C N 1 0.13350 410032.0 ; AA C_2 N 1 0.13350 410032.0 ; AA C_3 N 1 0.13350 410032.0 ; AA C N* 1 0.13830 354803.2 ; CYT,URA C_2 N* 1 0.13830 354803.2 ; CYT,URA C_3 N* 1 0.13830 354803.2 ; CYT,URA C NA 1 0.13880 349782.4 ; URAGUA C_2 NA 1 0.13880 349782.4 ; URAGUA C_3 NA 1 0.13880 349782.4 ; URAGUA C NC 1 0.13580 382417.6 ; CYT C_2 NC 1 0.13580 382417.6 ; CYT C_3 NC 1 0.13580 382417.6 ; CYT C O 1 0.12290 476976.0 ; URAGUA,CYT,AA C O_2 1 0.12290 476976.0 ; URAGUA,CYT,AA C O_3 1 0.12290 476976.0 ; URAGUA,CYT,AA C_2 O_2 1 0.12290 476976.0 ; C O2 1 0.12500 548940.8 ; GLU,ASP C_3 O2 1 0.12500 548940.8 ; GLU,ASP C OH 1 0.13640 376560.0 ; TYR NO ON 1 0.12250 460240.0 ; wlj nitro CT NO 1 0.14900 313800.0 ; wlj nitro CA NO 1 0.14600 334720.0 ; wlj nitro CA OH 1 0.13640 376560.0 ; CA OS 1 0.13640 376560.0 ; wlj CB OS 1 0.13600 284512.0 ; wlj CM OS 1 0.13700 376560.0 ; wlj CM OH 1 0.13700 376560.0 ; wlj CA O 1 0.13640 376560.0 ; CA O_2 1 0.13640 376560.0 ; C OS 1 0.13270 179075.2 ; J.Comp.Chem.1990,11,1181 SKF8 C_2 OS 1 0.13270 179075.2 ; J.Comp.Chem.1990,11,1181 SKF8 C* CB 1 0.14590 324678.4 ; TRP C* CT 1 0.14950 265265.6 ; TRP(OL) CU CT 1 0.15100 265265.6 ; CR CT 1 0.15100 265265.6 ; CS CT 1 0.14950 265265.6 ; wlj C* CW 1 0.13520 456892.8 ; TRP CA CR 1 0.13670 456892.8 ; from pyrrole- wlj CA CS 1 0.14240 392459.2 ; wlj CA CW 1 0.13670 456892.8 ; pyrrole- wlj CQ O 1 0.13640 376560.0 ; CQ O_2 1 0.13640 376560.0 ; CS CW 1 0.13670 456892.8 ; wj/nm CS CS 1 0.14240 392459.2 ; -idem- CS CB 1 0.14240 392459.2 ; -idem- CS HA 1 0.10800 307105.6 ; -idem- CU NB 1 0.13200 343088.0 ; -idem- CU CA 1 0.14210 392459.2 ; -idem- CU HA 1 0.10800 307105.6 ; -idem- NA NB 1 0.13490 334720.0 ; -idem- OS NB 1 0.13990 386601.6 ; -idem- OS CR 1 0.13570 386601.6 ; -idem- C3 C3 1 0.15260 217568.0 ; Ethane C3 NT 1 0.14480 319657.6 ; -idem- CT NT 1 0.14480 319657.6 ; -idem- NT NT 1 0.14450 292880.0 ; wlj CO OS 1 0.13800 267776.0 ; Acetal- wlj 2/93 CO C3 1 0.15260 217568.0 ; -idem- CW OS 1 0.13600 284512.0 ; Furan - wlj 4/97 C3 CM 1 0.15100 265265.6 ; THY(use std C-C) C3 N 1 0.14490 282001.6 ; TEST!!!! C3 N* 1 0.14750 282001.6 ; 9 methyl bases C3 N2 1 0.14630 282001.6 ; ARG(OL) C3 N3 1 0.14710 307105.6 ; C3 OH 1 0.14250 323004.8 ; SUG(OL),SER C3 OS 1 0.14250 267776.0 ; DMP C3 S 1 0.18100 185769.6 ; MET(OL) C3 SH 1 0.18100 185769.6 ; CYS(OL) CA CA 1 0.14000 392459.2 ; TRP,TYR,PHE CA C! 1 0.14000 392459.2 ; C! C! 1 0.14600 322168.0 ; wlj C! CS 1 0.14600 322168.0 ; wlj C! CU 1 0.14600 322168.0 ; wlj C! CV 1 0.14600 322168.0 ; wlj C! CW 1 0.14600 322168.0 ; wlj C! CR 1 0.14600 322168.0 ; wlj C! C 1 0.14600 322168.0 ; wlj C! C_2 1 0.14600 322168.0 ; wlj C! C_3 1 0.14600 322168.0 ; wlj C! CM 1 0.14600 322168.0 ; wlj C! NA 1 0.14400 322168.0 ; wlj CA CB 1 0.14040 392459.2 ; ADE CA CM 1 0.14330 357313.6 ; CA CN 1 0.14000 392459.2 ; TRP CA CT 1 0.15100 265265.6 ; PHE,TYR CA CY 1 0.14900 265265.6 ; wlj CW CT 1 0.15040 265265.6 ; jtr: HID CB-CG CV CT 1 0.15040 265265.6 ; jtr: HIE CB-CG CX CT 1 0.15040 265265.6 ; jtr: HIP CB-CG CX CA 1 0.15040 265265.6 ; CX CX 1 0.13700 435136.0 ; copy from CV-CW for HIP CX NA 1 0.13810 357313.6 ; jtr- HIP CX HA 1 0.10800 307105.6 ; jtr- HIP CA NY 1 0.13850 319657.6 ; jtr- neutral Arg; MLL CA NZ 1 0.12610 418400.0 ; jtr- neutral Arg; MLL NY H 1 0.10100 363171.2 ; jtr- neutral Arg; MLL NY H3 1 0.10100 363171.2 ; jtr- neutral Arg; MLL NZ H 1 0.10100 363171.2 ; jtr- neutral Arg; MLL NZ H3 1 0.10100 363171.2 ; jtr- neutral Arg; MLL CT NY 1 0.14480 319657.6 ; jtr- neutral Arg; MLL CA N2 1 0.13400 402500.8 ; ARG CQ N2 1 0.13400 402500.8 ; wlj CR N2 1 0.13400 402500.8 ; wlj CA NT 1 0.13400 402500.8 ; wj/rr anilines CA NA 1 0.13810 357313.6 ; GUA CQ N 1 0.13810 357313.6 ; wlj CA NC 1 0.13390 404174.4 ; ADE,GUA,CYT C! NC 1 0.13390 404174.4 ; wlj NC NC 1 0.13200 418400.0 ; wlj pyridazine NC NZ 1 0.12400 460240.0 ; wlj azide NZ NZ 1 0.11200 460240.0 ; wlj azide CA HA 1 0.10800 307105.6 ; PHE, etc. CB CB 1 0.13700 435136.0 ; ADE,GUA CR CS 1 0.13700 435136.0 ; wj CV CW 1 0.13700 435136.0 ; wlj imidazole CB CN 1 0.14190 374049.6 ; TRP CB N* 1 0.13740 364844.8 ; ADE,GUA CB NA 1 0.13740 364844.8 ; wlj CB NB 1 0.13910 346435.2 ; ADE,GUA,HIS CB NC 1 0.13540 385764.8 ; ADE,GUA CR NC 1 0.13540 385764.8 ; wj CW CW 1 0.13750 428441.6 ; CK HA 1 0.10800 284512.0 ; CK H5 1 0.10800 307105.6 ; CK N* 1 0.13710 368192.0 ; CK NA 1 0.13710 368192.0 ; CK NB 1 0.13040 442667.2 ; CM CM 1 0.13400 459403.2 ; wlj CM C= 1 0.13400 459403.2 ; wlj CW C= 1 0.13650 459403.2 ; C= C= 1 0.14600 322168.0 ; wlj 1,3-diene 3/97 C C 1 0.15100 292880.0 ; wlj oxalic acid, etc. C C_2 1 0.15100 292880.0 ; wlj oxalic acid, etc. C C_3 1 0.15100 292880.0 ; wlj oxalic acid, etc. C= C 1 0.14600 322168.0 ; wlj acrolein C= C_2 1 0.14600 322168.0 ; wlj acrolein C= C_3 1 0.14600 322168.0 ; wlj acrolein CT C+ 1 0.14600 445847.0 ; wlj- JACS 94, 4632 (1972) C+ HC 1 0.10840 445847.0 ; wlj- -idem- CM CT 1 0.15100 265265.6 ; wlj C= CT 1 0.15100 265265.6 ; wlj CM HC 1 0.10800 284512.0 ; wlj CM H4 1 0.10800 307105.6 ; C= HC 1 0.10800 284512.0 ; wlj HC C 1 0.10900 284512.0 ; wlj 7/96 HC C_2 1 0.10900 284512.0 ; wlj 7/96 HC C_3 1 0.10900 284512.0 ; wlj 7/96 CT CZ 1 0.14700 326352.0 ; wlj 9/98 do 11/98 CA CZ 1 0.14510 334720.0 ; wlj 9/98 CY CZ 1 0.14510 334720.0 ; wlj CZ NZ 1 0.11570 543920.0 ; wlj 9/98 CZ CZ 1 0.12100 962320.0 ; do 11/98- JPOC, 9, 191 (1996) HC CZ 1 0.10800 351456.0 ; do 01/99- JPOC, 9, 191 (1996) CM N* 1 0.13650 374886.4 ; CM NA 1 0.13650 374886.4 ; copy from above for CytH+ (jtr 5-14-91) CN NA 1 0.13800 358150.4 ; TRP CQ HA 1 0.10800 307105.6 ; CQ H5 1 0.10800 307105.6 ; CQ NC 1 0.13240 420073.6 ; CR HA 1 0.10800 307105.6 ; CR H5 1 0.10800 307105.6 ; CR NA 1 0.13430 399153.6 ; HIS CR NB 1 0.13350 408358.4 ; HIS(MOD) CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file CT CT_2 1 0.15290 224262.4 ; AA Calpha CT CT_3 1 0.15290 224262.4 ; Pro CD CT CT_4 1 0.15290 224262.4 ; Trifluoroethanol CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file CT_2 HC 1 0.10900 284512.0 ; AA Calpha CT_3 HC 1 0.10900 284512.0 ; Pro CD CT_4 HC 1 0.10900 284512.0 ; Trifluoroethanol CT_3 N 1 0.14490 282001.6 ; Pro CD CT_3 NT 1 0.14490 282001.6 ; Pro CD CT N 1 0.14490 282001.6 ; CT_2 N 1 0.14490 282001.6 ; AA Calpha CT_2 NT 1 0.14480 319657.6 ; -idem- CT NC 1 0.14490 282001.6 ; wj azide CY N 1 0.14490 282001.6 ; wj CT N* 1 0.14750 282001.6 ; CT NA 1 0.14750 282001.6 ; copy from above for CytH+ (jtr 5-14-91) CT N2 1 0.14630 282001.6 ; ARG(OL) CT N3 1 0.14710 307105.6 ; LYS(OL) CT_2 N3 1 0.14710 307105.6 ; AA Calpha CT_3 N3 1 0.14710 307105.6 ; Pro CD CT OH 1 0.14100 267776.0 ; CT_4 OH 1 0.14100 267776.0 ; ifluoroethanol NT OH 1 0.14500 267776.0 ; wlj NT OS 1 0.14500 267776.0 ; wlj N OH 1 0.13800 334720.0 ; wlj CT OS 1 0.14100 267776.0 ; CT S 1 0.18100 185769.6 ; CYX(OL) CY S 1 0.18100 185769.6 ; wj CR S 1 0.17600 209200.0 ; wlj CW S 1 0.17400 209200.0 ; wlj CA SH 1 0.17400 209200.0 ; wlj CT SH 1 0.18100 185769.6 ; CYS(OL) CT Cl 1 0.17810 205016.0 ; wlj- from MM2 (Tet 31, 1971 (75)) CA Cl 1 0.17250 251040.0 ; wlj CM Cl 1 0.17250 251040.0 ; wlj C Cl 1 0.17900 251040.0 ; wlj C_2 Cl 1 0.17900 251040.0 ; wlj C_3 Cl 1 0.17900 251040.0 ; wlj CZ Cl 1 0.16370 276144.0 ; wlj CT Br 1 0.19450 205016.0 ; wlj CA Br 1 0.18700 251040.0 ; wlj CM Br 1 0.19000 251040.0 ; wlj C Br 1 0.19800 251040.0 ; C_2 Br 1 0.19800 251040.0 ; C_3 Br 1 0.19800 251040.0 ; CZ Br 1 0.17840 276144.0 ; wlj CA I 1 0.20800 230120.0 ; wlj CV HA 1 0.10800 307105.6 ; CV H4 1 0.10800 307105.6 ; CV NB 1 0.13940 343088.0 ; ADE,GUA,HIS CW NB 1 0.13940 343088.0 ; CW H4 1 0.10800 307105.6 ; CW HA 1 0.10800 307105.6 ; pyrrole- wlj CW NA 1 0.13810 357313.6 ; TRP,HIS CW N 1 0.13810 357313.6 ; CY CY 1 0.15090 217568.0 ; cyclopropanes- wlj CY CT 1 0.15100 234304.0 ; -idem- CY HC 1 0.10880 284512.0 ; -idem- H N 1 0.10100 363171.2 ; H N3 1 0.10100 363171.2 ; H N* 1 0.10100 363171.2 ; H N2 1 0.10100 363171.2 ; URA,GUA,HIS H NA 1 0.10100 363171.2 ; URA,GUA,HIS H NT 1 0.10100 363171.2 ; H3 N2 1 0.10100 363171.2 ; ADE,GUA,CYT,GLN,ASN,ARG H3 N3 1 0.10100 363171.2 ; LYS(OL) HO OH 1 0.09450 462750.4 ; SUG(OL) wlj mod 0.96-> 0.945 HO OS 1 0.09450 462750.4 ; SUG(OL) 6/6/94 HS SH 1 0.13360 229283.2 ; CYS(OL) LP S 1 0.06790 502080.0 ; LP SH 1 0.06790 502080.0 ; O2 P 1 0.14800 439320.0 ; SUG(OL) O P 1 0.14800 439320.0 ; OH P 1 0.16100 192464.0 ; SUG(OL) OS P 1 0.16100 192464.0 ; SUG(OL) CT P 1 0.18430 177401.6 ; wlj 11/95 MM3 based JACS 114, 8536 (92) CA P 1 0.17800 184096.0 ; CT P+ 1 0.18200 177401.6 ; wlj 9/97 S S 1 0.20380 138908.8 ; CYX(OL) SCHERAGA CT C3 1 0.15260 217568.0 ; Added DSM (from C3-CH) CA NB 1 0.13910 346435.2 ; Added DSM (from CB-NB) CA N 1 0.13810 357313.6 ; Added DSM (from GUA) CB CT 1 0.15100 265265.6 ; Added DSM (from CA-CT) CT F 1 0.13320 307105.6 ; PAK CT-F for CHF3 (emd 5-09-94) CA F 1 0.13540 351456.0 ; wlj CM F 1 0.13400 351456.0 ; wlj CZ F 1 0.12790 376560.0 ; wlj C F 1 0.13570 351456.0 ; wlj C_2 F 1 0.13570 351456.0 ; wlj C_3 F 1 0.13570 351456.0 ; wlj CT CO 1 0.15290 224262.4 ; =CT-CT- wd 3/95 OH CO 1 0.13800 267776.0 ; =CO-OS- wd 3/96 HC CO 1 0.10900 284512.0 ; =CT-HC- wd 3/95 SY C3 1 0.18100 185769.6 ; SY CA 1 0.17700 284512.0 ; SY OY 1 0.14400 585760.0 ; SZ OY 1 0.15300 585760.0 ; SY N 1 0.16700 363171.2 ; SY CT 1 0.17700 284512.0 ; SZ CT 1 0.17900 284512.0 ; U OU 1 0.18000 418400.0 ; J Phys Chem 97, 5685 (1993) CA S 1 0.17600 209200.0 ; thioanisole CM S 1 0.17600 209200.0 ; CM CY 1 0.15100 265265.6 ; CY NT 1 0.14480 319657.6 ; SY NT 1 0.17700 284512.0 ; C NT 1 0.15220 265265.6 ; C_2 NT 1 0.15220 265265.6 ; C_3 NT 1 0.15220 265265.6 ; C CW 1 0.14900 334720.0 ; C_2 CW 1 0.14900 334720.0 ; C_3 CW 1 0.14900 334720.0 ; [ constrainttypes ] ; this section is implemented manually from bond & angle values ; account for larger inertia with heavy hydrogens #ifdef HEAVY_H ; constraints for the rigid NH3 groups MNH3 CT 2 0.188929 MNH3 CT_2 2 0.188929 MNH3 MNH3 2 0.160473 ; constraints for rigid umbrella-shaped NH2 group MNH2 CT 2 0.175302 MNH2 CT_2 2 0.175302 MNH2 MNH2 2 0.135084 ; constraints for 1st type rigid CH3 (angle *-CT-HC is 109.5) MCH3A C 2 0.203533 MCH3A C_2 2 0.203533 MCH3A CW 2 0.201930 MCH3A CV 2 0.201930 MCH3A CS 2 0.201129 MCH3A CA 2 0.202464 MCH3A CB 2 0.202464 MCH3A N 2 0.197052 MCH3A S 2 0.229582 MCH3A MCH3A 2 0.184320 ; constraints for 2nd type rigid CH3 (angle *-CT-HC is 110.7) MCH3B CT 2 0.205384 MCH3B CT_2 2 0.205384 MCH3B CT_3 2 0.205384 MCH3B CO 2 0.205384 MCH3B MCH3B 2 0.182913 #else ; no heavy hydrogens. ; constraints for the rigid NH3 groups MNH3 CT 2 0.158255 MNH3 CT_2 2 0.158255 MNH3 MNH3 2 0.080236 ; constraints for rigid umbrella-shaped NH2 group MNH2 CT 2 0.152820 MNH2 CT_2 2 0.152820 MNH2 MNH2 2 0.067542 ; constraints for 1st type rigid CH3 (angle *-CT-HC is 109.5) MCH3A C 2 0.166040 MCH3A C_2 2 0.166040 MCH3A CW 2 0.164312 MCH3A CV 2 0.164312 MCH3A CS 2 0.163448 MCH3A CA 2 0.164888 MCH3A CB 2 0.164888 MCH3A N 2 0.159040 MCH3A S 2 0.193874 MCH3A MCH3A 2 0.092160 ; constraints for 2nd type rigid CH3 (angle *-CT-HC is 110.7) MCH3B CT 2 0.167031 MCH3B CT_2 2 0.167031 MCH3B CT_3 2 0.167031 MCH3B CO 2 0.167031 MCH3B MCH3B 2 0.091456 #endif ; angle-derived constraints for OH and SH groups in proteins ; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C. N HO 2 0.18682 C HO 2 0.19393 CA HO 2 0.19393 CT HO 2 0.19305 CO HO 2 0.19039 CT HS 2 0.23593 CA HS 2 0.23018 [ angletypes ] ; i j k func th0 cth HW OW HW 1 109.500 627.600 ; For TIP4F Water - wj 1/98 HW OW LP 1 54.750 418.400 ; For TIP4F Water - wj 1/98 OU U OU 1 180.000 1255.200 ; J Phys Chem 97, 5685 (1993) HC C* CW 1 126.800 292.880 ; HC C* CB 1 126.800 292.880 ; HC CS CW 1 126.800 292.880 ; HC CS CB 1 126.800 292.880 ; HA CA CW 1 126.900 292.880 ; wlj - pyrrole HC C= CW 1 122.000 292.880 ; wlj HA CW CA 1 130.700 292.880 ; wlj HA CW C= 1 130.700 292.880 ; wlj HA CW NA 1 121.600 292.880 ; wlj CT CW NA 1 121.600 585.760 ; wlj C! CW NA 1 121.600 585.760 ; wlj CT CW OS 1 121.600 585.760 ; wlj C! CW OS 1 121.600 585.760 ; wlj CA CW NA 1 121.600 585.760 ; wlj HA CW CV 1 130.700 292.880 ; wlj - imidazole HA CV CW 1 128.200 292.880 ; wlj HC CT CZ 1 108.500 292.880 ; wlj CT CT CR 1 114.000 527.184 ; CT CT CZ 1 112.700 488.273 ; wlj CT CZ CZ 1 180.000 1255.200 ; do 11/98 - JPOC, 9, 191(1996) CA CZ CZ 1 180.000 1338.880 ; wlj HC CZ CZ 1 180.000 937.216 ; do 1/99 - JPOC, 9, 191(1996) CA CA CZ 1 120.000 585.760 ; wlj CA CA CR 1 120.000 527.184 ; CA CA CX 1 120.000 711.280 ; CA CR NB 1 111.000 585.760 ; wlj CT CZ NZ 1 180.000 1255.200 ; wlj N2 CZ NZ 1 180.000 1255.200 ; wlj CA CZ NZ 1 180.000 1255.200 ; wlj CT CX NA 1 121.600 585.760 ; jtr - copy from CT-CW-NA for HIP HA CX CX 1 130.700 292.880 ; jtr - copy from HA-CW-CV for HIP CX CX NA 1 106.300 585.760 ; jtr - copy from CV-CW-NA for HIP CX NA CR 1 109.800 585.760 ; jtr - copy from CW-NA-CR for HIP C3 C N 1 116.600 585.760 ; ACET(OL) BENEDETTI C3 C O 1 120.400 669.440 ; ACET(OL) C3 C O_2 1 120.400 669.440 ; ACET(OL) C3 C O_3 1 120.400 669.440 ; ACET(OL) C3 C_2 O_2 1 120.400 669.440 ; ACET(OL) C3 C_3 O2 1 117.000 585.760 ; GLU(OL) SCH JPC 79,2379 CA C CA 1 120.000 711.280 ; TYR(OL) GELIN CA C_2 CA 1 120.000 711.280 ; TYR(OL) GELIN CA C OH 1 120.000 585.760 ; TYR(OL) GELIN CA CA O 1 120.000 585.760 ; CA CA OH 1 120.000 585.760 ; CA CA SH 1 120.000 585.760 ; wlj CA CA OS 1 120.000 585.760 ; wlj CM CM OS 1 123.000 585.760 ; wlj C= CM OS 1 123.000 585.760 ; wlj CM CM OH 1 123.000 585.760 ; wlj C= CM OH 1 123.000 585.760 ; wlj CB C NA 1 111.300 585.760 ; GUA CB C_2 NA 1 111.300 585.760 ; GUA CB C O 1 128.800 669.440 ; GUA CB C O_2 1 128.800 669.440 ; GUA CB C O_3 1 128.800 669.440 ; GUA CB C_2 O_2 1 128.800 669.440 ; GUA CB C N 1 111.300 585.760 ; wlj CS C O 1 128.200 669.440 ; wj CS C O_2 1 128.200 669.440 ; wj CS C O_3 1 128.200 669.440 ; wj CS C_2 O_2 1 128.200 669.440 ; wj CM C NA 1 114.100 585.760 ; THY CM C_2 NA 1 114.100 585.760 ; THY CM C O 1 125.300 669.440 ; THY CM C O_2 1 125.300 669.440 ; THY CM C O_3 1 125.300 669.440 ; THY CM C_2 O_2 1 125.300 669.440 ; THY CM C C 1 117.200 669.440 ; (JP 1-6-91) CM C C_2 1 117.200 669.440 ; (JP 1-6-91) CM C C_3 1 117.200 669.440 ; (JP 1-6-91) CM C_2 C 1 117.200 669.440 ; (JP 1-6-91) CM C_2 C_2 1 117.200 669.440 ; (JP 1-6-91) CM C_2 C_3 1 117.200 669.440 ; (JP 1-6-91) CM C OH 1 108.000 585.760 ; C= C O 1 124.000 669.440 ; wlj C= C O_2 1 124.000 669.440 ; wlj C= C O_3 1 124.000 669.440 ; wlj C= C_2 O_2 1 124.000 669.440 ; wlj C= C OH 1 108.000 585.760 ; C= C HC 1 116.000 669.440 ; wlj C= C_2 HC 1 116.000 669.440 ; wlj CT C N 1 116.600 585.760 ; CT_2 C N 1 116.600 585.760 ; CA C N 1 115.500 585.760 ; wlj 8/97 benzamide CM C N 1 115.500 585.760 ; wlj CT C O 1 120.400 669.440 ; CT C O_2 1 120.400 669.440 ; CT C O_3 1 120.400 669.440 ; CT C_2 O_2 1 120.400 669.440 ; CT_2 C O 1 120.400 669.440 ; CT_2 C O_2 1 120.400 669.440 ; CT_2 C O_3 1 120.400 669.440 ; CT_2 C_2 O_2 1 120.400 669.440 ; 4 CA C O 1 120.400 669.440 ; wlj CA C O_2 1 120.400 669.440 ; wlj CA C O_3 1 120.400 669.440 ; wlj CA C_2 O_2 1 120.400 669.440 ; wlj CT NO ON 1 117.500 669.440 ; wlj nitro CA NO ON 1 117.500 669.440 ; wlj nitro CT CT NO 1 111.100 527.184 ; wlj nitro HC CT NO 1 105.000 292.880 ; wlj nitro CA CA NO 1 120.000 711.280 ; wlj nitro HC C N 1 114.000 334.720 ; wlj HC C OS 1 115.000 334.720 ; -idem- HC C_2 OS 1 115.000 334.720 ; -idem- HC C OH 1 115.000 334.720 ; -idem- O C HC 1 123.000 292.880 ; wlj O_2 C HC 1 123.000 292.880 ; wlj O_3 C HC 1 123.000 292.880 ; wlj O_2 C_2 HC 1 123.000 292.880 ; wlj NC C HC 1 122.000 292.880 ; wlj NC C_2 HC 1 122.000 292.880 ; wlj CT C OH 1 108.000 585.760 ; RCOOH wlj 2/15/95 CT_2 C OH 1 108.000 585.760 ; CT C CT 1 116.000 585.760 ; wlj 7/96 CT C_2 CT 1 116.000 585.760 ; wlj 7/96 CT C CA 1 116.000 585.760 ; wlj CT C_2 CA 1 116.000 585.760 ; wlj C= C CT 1 116.000 585.760 ; wlj C= C_2 CT 1 116.000 585.760 ; wlj CT C_3 O2 1 117.000 585.760 ; GLU(OL) SCH JPC 79,2379 CT_2 C_3 O2 1 117.000 585.760 ; GLU(OL) SCH JPC 79,2379 CT CT Cl 1 109.800 577.392 ; wlj - from MM2 C CT Cl 1 109.800 577.392 ; wlj C CT_2 Cl 1 109.800 577.392 ; CA CA Cl 1 120.000 627.600 ; CM CM Cl 1 121.500 627.600 ; Cl CM HC 1 114.000 502.080 ; Cl CT Cl 1 111.700 652.704 ; HC CT Cl 1 107.600 426.768 ; CT CT Br 1 110.000 577.392 ; C CT Br 1 109.800 577.392 ; C_2 CT Br 1 109.800 577.392 ; C_3 CT Br 1 109.800 577.392 ; CT C Cl 1 109.000 627.600 ; CT C_2 Cl 1 109.000 627.600 ; wlj CT C Br 1 109.000 627.600 ; wlj CT C_2 Br 1 109.000 627.600 ; wlj O C Cl 1 119.000 627.600 ; wlj O_2 C Cl 1 119.000 627.600 ; wlj O_3 C Cl 1 119.000 627.600 ; wlj O_2 C_2 Cl 1 119.000 627.600 ; wlj O C Br 1 119.000 627.600 ; wlj O_2 C Br 1 119.000 627.600 ; wlj O_3 C Br 1 119.000 627.600 ; wlj O_2 C_2 Br 1 119.000 627.600 ; wlj CA CA Br 1 120.000 627.600 ; wlj CM CM Br 1 120.000 627.600 ; wlj Br CM HC 1 114.000 502.080 ; wlj Br CT Br 1 111.700 652.704 ; wlj HC CT Br 1 107.600 426.768 ; wlj CA CA I 1 120.000 627.600 ; wlj CA CA F 1 120.000 669.440 ; wlj CM CM F 1 121.500 669.440 ; wlj C CM F 1 121.500 669.440 ; wlj F CM HC 1 112.000 418.400 ; wlj F CM F 1 108.000 669.440 ; wlj F C O 1 121.000 669.440 ; wlj F C O_2 1 121.000 669.440 ; wlj F C O_3 1 121.000 669.440 ; wlj F C_2 O_2 1 121.000 669.440 ; wlj F C CT 1 111.000 669.440 ; wlj F C_2 CT 1 111.000 669.440 ; wlj N C O 1 122.900 669.440 ; AA(OL) N C O_2 1 122.900 669.440 ; AA(OL) N C O_3 1 122.900 669.440 ; AA(OL) N C_2 O_2 1 122.900 669.440 ; AA(OL) N C N 1 114.200 585.760 ; copy from above for Urea (jtr 5-14-91) N C_2 N 1 114.200 585.760 ; copy from above for Urea (jtr 5-14-91) N* C NA 1 115.400 585.760 ; URA N* C_2 NA 1 115.400 585.760 ; URA N* C NC 1 118.600 585.760 ; CYT N* C_2 NC 1 118.600 585.760 ; CYT NA C NA 1 118.600 585.760 ; copy from above for CytH+ (jtr 5-14-91) NA C_2 NA 1 118.600 585.760 ; copy from above for CytH+ (jtr 5-14-91) N* C O 1 120.900 669.440 ; URA,CYT N* C O_2 1 120.900 669.440 ; URA,CYT N* C O_3 1 120.900 669.440 ; URA,CYT N* C_2 O_2 1 120.900 669.440 ; URA,CYT NA C O 1 120.600 669.440 ; URA(2),GUA NA C O_2 1 120.600 669.440 ; URA(2),GUA NA C O_3 1 120.600 669.440 ; URA(2),GUA NA C_2 O_2 1 120.600 669.440 ; URA(2),GUA NC C O 1 122.500 669.440 ; CYT NC C O_2 1 122.500 669.440 ; CYT NC C O_3 1 122.500 669.440 ; CYT NC C_2 O_2 1 122.500 669.440 ; CYT NC C NA 1 118.600 585.760 ; NC C_2 NA 1 118.600 585.760 ; NA CM H4 1 119.100 292.880 ; N CA HA 1 119.100 292.880 ; wlj ON NO ON 1 125.000 669.440 ; wlj nitro O_3 C OH 1 121.000 669.440 ; RCOOH wlj 2/15/95 O2 C_3 O2 1 126.000 669.440 ; GLU(OL) SCH JPC 79,2379 CB C* CT 1 128.600 585.760 ; TRP(OL) CB C* CW 1 106.400 711.280 ; TRP(OL) CT C* CW 1 125.000 585.760 ; TRP(OL) CB CS CT 1 128.600 585.760 ; CB CS CW 1 106.400 711.280 ; CT CS CW 1 125.000 585.760 ; TRP(OL) CT CT NT 1 109.470 470.281 ; wlj - MM3 based - JACS 112, 8314 (90) C3 CT NT 1 109.470 470.281 ; wlj - MM3 based - JACS 112, 8314 (90) CT CT_2 NT 1 109.470 470.281 ; C CA CA 1 120.000 711.280 ; TYR(OL) C_2 CA CA 1 120.000 711.280 ; TYR(OL) C_3 CA CA 1 120.000 711.280 ; TYR(OL) C CA HA 1 120.000 292.880 ; C_2 CA HA 1 120.000 292.880 ; C_3 CA HA 1 120.000 292.880 ; CA CA CA 1 120.000 527.184 ; PHE(OL) CA C! CA 1 120.000 527.184 ; wlj CA C! C! 1 120.000 527.184 ; wlj CA CA C! 1 120.000 527.184 ; wlj CA C! CR 1 120.000 527.184 ; wlj CA C! CS 1 120.000 527.184 ; wlj CA C! CW 1 120.000 527.184 ; wlj CA C! CU 1 120.000 527.184 ; wlj CA C! CV 1 120.000 527.184 ; wlj CA CA CB 1 120.000 527.184 ; TRP(OL) CA CA CN 1 120.000 711.280 ; TRP(OL) CA CA CM 1 124.000 585.760 ; wlj/mp CA CM CT 1 119.700 711.280 ; wlj/mp CA CM C= 1 117.000 711.280 ; CA CA CT 1 120.000 585.760 ; PHE(OL) CA CA NT 1 120.100 585.760 ; wlj/rr anilines CA CA HA 1 120.000 292.880 ; C! CA HA 1 120.000 292.880 ; wlj CT NC CQ 1 118.600 585.760 ; CT NC NZ 1 120.000 585.760 ; wlj azide NC NZ NZ 1 180.000 836.800 ; wlj azide CT CT NC 1 109.000 543.920 ; wlj azide NC CA HA 1 116.000 292.880 ; wlj 12/96 based on pyridine CA CA NC 1 124.000 585.760 ; wlj -idem- CA C! NC 1 124.000 585.760 ; wlj -idem- C! CA NC 1 124.000 585.760 ; wlj -idem- C! C! NC 1 124.000 585.760 ; wlj -idem- CA NC CA 1 117.000 585.760 ; wlj -idem- CA NC C! 1 117.000 585.760 ; wlj -idem- CA NC CY 1 125.800 585.760 ; wlj CA CA CW 1 107.400 585.760 ; wlj 1/97 based on pyrrole CV NA H 1 120.000 292.880 ; CW NA CW 1 109.800 585.760 ; wlj -idem- CW NA CT 1 125.800 585.760 ; CV CW NA 1 106.300 585.760 ; wlj 1/97 based on imidazole CV CW N 1 106.300 585.760 ; wlj imidazole CW CV NB 1 111.000 585.760 ; wlj -idem- CW NA CR 1 109.800 585.760 ; wlj -idem- CB NA CR 1 109.800 585.760 ; wlj CW C= C= 1 106.000 292.880 ; wlj CA NA CK 1 109.800 585.760 ; wlj NC CA CT 1 116.000 585.760 ; wlj NC CQ CT 1 115.500 585.760 ; wlj NC CQ O 1 122.500 669.440 ; NB CV CT 1 124.500 585.760 ; wlj CA CV NB 1 111.000 585.760 ; wlj CA NC NC 1 117.000 585.760 ; wlj pyridazine CT NC NC 1 117.000 585.760 ; wlj azo OS CW CS 1 110.600 585.760 ; wlj OS CW CA 1 110.600 585.760 ; wlj OS CW C= 1 110.000 585.760 ; wlj furan CW OS CW 1 106.500 585.760 ; wlj furan CW OS CB 1 106.500 585.760 ; wlj furan CR OS CB 1 106.500 585.760 ; wlj furan OS CW HA 1 113.400 292.880 ; wlj furan S CW HA 1 113.400 292.880 ; wlj S CR CA 1 111.000 585.760 ; wlj S CR HA 1 113.400 292.880 ; wlj S CW CV 1 111.000 585.760 ; wlj S CW CS 1 111.000 585.760 ; wlj S CW N 1 115.000 585.760 ; NA CW CS 1 107.700 585.760 ; wj/nm CW CS CS 1 107.300 585.760 ; -idem- CW CS HA 1 125.700 292.880 ; -idem- CW CS C! 1 125.700 585.760 ; -idem- CS CW C! 1 132.100 585.760 ; -idem- CS CS C! 1 127.500 585.760 ; -idem- CS CW HA 1 132.100 292.880 ; -idem- CS CW CT 1 132.100 585.760 ; -idem- CS CW CA 1 132.100 585.760 ; -idem- CS CS HA 1 127.500 292.880 ; -idem- CU NB NA 1 104.100 585.760 ; -idem- CW NB NA 1 104.100 585.760 ; -idem- NB CU HA 1 118.900 292.880 ; -idem- NB CU CA 1 111.900 585.760 ; -idem- NB CU CT 1 118.900 585.760 ; -idem- NB CW CT 1 118.900 585.760 ; -idem- NB CW S 1 115.000 585.760 ; CU CS CW 1 103.800 585.760 ; -idem- CW CS CW 1 103.800 585.760 ; -idem- NB CU CS 1 111.900 585.760 ; -idem- NB CW CS 1 111.900 585.760 ; -idem- CA CU HA 1 128.600 292.880 ; -idem- CU CA HA 1 128.200 292.880 ; -idem- CU CA CW 1 103.800 585.760 ; -idem- CU NB OS 1 105.300 585.760 ; -idem- NB NA CW 1 113.100 468.608 ; -idem- CB NA NB 1 113.100 468.608 ; -idem- CR NA CT 1 125.800 585.760 ; CR NA NB 1 113.100 468.608 ; -idem- NB NA H 1 118.400 468.608 ; -idem- NB NA CA 1 118.400 585.760 ; -idem- NB NA CT 1 118.400 585.760 ; -idem- CW OS NB 1 108.900 585.760 ; -idem- NB CR OS 1 115.000 585.760 ; -idem- NB CR S 1 115.000 585.760 ; -idem- CR OS CW 1 104.000 585.760 ; -idem- CV CW OS 1 108.000 585.760 ; -idem- HA CR OS 1 117.000 292.880 ; -idem- OS CM HC 1 114.500 292.880 ; CB CA HA 1 120.000 292.880 ; CB CA N2 1 123.500 585.760 ; ADE CB CA NC 1 117.300 585.760 ; ADE CM CA N2 1 120.100 585.760 ; CA CA N2 1 120.100 585.760 ; wlj CM CA NC 1 121.500 585.760 ; CM CA NA 1 121.500 585.760 ; copy from above for CytH+ (jtr 5-14-91) CN CA HA 1 120.000 292.880 ; NY CA NY 1 111.800 585.760 ; jtr: neutral ARG NZ CA NY 1 124.100 585.760 ; jtr: neutral ARG CA NZ H 1 113.000 292.880 ; jtr: neutral ARG CA NZ H3 1 113.000 292.880 ; jtr: neutral ARG CA NY H 1 112.500 418.400 ; jtr: neutral ARG CA NY H3 1 112.500 418.400 ; jtr: neutral ARG CA NY CT 1 120.500 418.400 ; jtr: neutral ARG H NY H 1 106.400 364.845 ; jtr: neutral ARG H3 NY H3 1 106.400 364.845 ; jtr: neutral ARG CT NY H 1 109.500 292.880 ; jtr: neutral ARG CT NY H3 1 109.500 292.880 ; jtr: neutral ARG CT CT NY 1 111.200 669.440 ; jtr: neutral ARG HC CT NY 1 109.500 292.880 ; jtr: neutral ARG N2 CA N2 1 120.000 585.760 ; ARG(OL) N2 CA NA 1 116.000 585.760 ; GUA N2 CA NC 1 119.300 585.760 ; ADE,GUA N2 CQ NC 1 119.300 585.760 ; wlj N2 CQ N 1 116.000 585.760 ; wlj NA CA NC 1 123.300 585.760 ; GUA C CB CB 1 119.200 711.280 ; GUA C_2 CB CB 1 119.200 711.280 ; GUA C_3 CB CB 1 119.200 711.280 ; GUA C CB NB 1 130.000 585.760 ; GUA C_2 CB NB 1 130.000 585.760 ; GUA C_3 CB NB 1 130.000 585.760 ; GUA N CQ NC 1 123.300 585.760 ; wlj C CS CW 1 130.000 585.760 ; wj C_2 CS CW 1 130.000 585.760 ; wj C_3 CS CW 1 130.000 585.760 ; wj C CB CW 1 130.000 585.760 ; wj C_2 CB CW 1 130.000 585.760 ; wj C_3 CB CW 1 130.000 585.760 ; wj C* CB CA 1 134.900 711.280 ; TRP(OL) CA CB CA 1 134.900 711.280 ; TRP(OL) C* CB CN 1 108.800 711.280 ; TRP(OL) CS CB CA 1 134.900 711.280 ; CS CB CN 1 108.800 711.280 ; CA CB CB 1 117.300 711.280 ; ADE CA CB CN 1 116.200 711.280 ; TRP CA CB NB 1 132.400 585.760 ; ADE CB CB N* 1 106.200 585.760 ; GUA,ADE CB CB NA 1 106.200 585.760 ; wlj CS CR NA 1 106.200 585.760 ; wj CR CS CW 1 110.400 585.760 ; wj CB CB NC 1 127.700 585.760 ; GUA,ADE CB CB N 1 127.700 585.760 ; wj CS CR NC 1 127.700 585.760 ; wj N* CB NC 1 126.200 585.760 ; GUA,ADE NA CB NC 1 126.200 585.760 ; wlj NB CB N 1 126.200 585.760 ; wj NB CR N 1 126.200 585.760 ; wj NA CR NC 1 126.200 585.760 ; wj CT CW CV 1 130.700 585.760 ; jtr: HID CB-CG-CD2 CT CV CW 1 130.700 585.760 ; jtr: HIE CB-CG-CD2 CT CX CX 1 130.700 585.760 ; jtr: HIP CB-CG-CD2 CT CW CW 1 120.000 585.760 ; CW CW NA 1 120.000 585.760 ; CA CA NA 1 108.700 585.760 ; TRP(OL) N* CK NB 1 113.900 585.760 ; NA CK NB 1 113.900 585.760 ; wlj NA CK H5 1 123.050 292.880 ; N* CK H5 1 123.050 292.880 ; NB CK H5 1 123.050 292.880 ; C CM C3 1 119.700 711.280 ; THY C_2 CM C3 1 119.700 711.280 ; THY C_3 CM C3 1 119.700 711.280 ; THY C CM CM 1 120.700 711.280 ; C_2 CM CM 1 120.700 711.280 ; C_3 CM CM 1 120.700 711.280 ; C CM CT 1 119.700 585.760 ; C_2 CM CT 1 119.700 585.760 ; C_3 CM CT 1 119.700 585.760 ; C CA CT 1 119.700 585.760 ; wlj C_2 CA CT 1 119.700 585.760 ; wlj C_3 CA CT 1 119.700 585.760 ; wlj C CM HC 1 119.700 292.880 ; C_2 CM HC 1 119.700 292.880 ; C_3 CM HC 1 119.700 292.880 ; CA CM CM 1 117.000 711.280 ; CA CM HC 1 123.300 292.880 ; CM CM CT 1 124.000 585.760 ; wlj CM C= C= 1 124.000 585.760 ; wlj CM C= C 1 118.700 585.760 ; wlj CM C= C_2 1 118.700 585.760 ; wlj CM C= C_3 1 118.700 585.760 ; wlj CM C= CT 1 124.000 585.760 ; wlj C= C= CT 1 124.000 585.760 ; wlj CT CM C= 1 124.000 585.760 ; mwm CM CT CM 1 112.400 527.184 ; mwm CM CT OS 1 120.000 585.760 ; CM CT OH 1 109.500 418.400 ; CM CM HC 1 120.000 292.880 ; wlj CM CM H4 1 119.700 292.880 ; CM C= HC 1 120.000 292.880 ; wlj C= CM HC 1 120.000 292.880 ; wlj C= C= HC 1 120.000 292.880 ; wlj C C= HC 1 119.700 292.880 ; C_2 C= HC 1 119.700 292.880 ; C_3 C= HC 1 119.700 292.880 ; CT C HC 1 115.000 292.880 ; wlj CT C_2 HC 1 115.000 292.880 ; wlj CA C HC 1 115.000 292.880 ; wlj CA C_2 HC 1 115.000 292.880 ; wlj CT CM HC 1 117.000 292.880 ; wlj HC CM HC 1 117.000 292.880 ; wlj CT CM CT 1 130.000 585.760 ; wlj CT C+ CT 1 120.000 1445.990 ; wlj JACS 94, 4632 (1972) CT C+ HC 1 120.000 1204.992 ; wlj -idem- CT CT C+ 1 105.000 527.184 ; wlj HC CT C+ 1 105.000 292.880 ; wlj CM CM N* 1 121.200 585.760 ; CM CM NA 1 121.200 585.760 ; copy from above for CytH+ (jtr 5-14-91) HC CM N* 1 119.100 292.880 ; HC CM NA 1 119.100 292.880 ; copy from above for CytH+ (jtr 5-14-91) CA CN CB 1 122.700 711.280 ; TRP CA CN NA 1 132.800 585.760 ; TRP(OL) CB CA CW 1 106.400 527.184 ; CB CA CT 1 128.600 585.760 ; CB CN NA 1 104.400 585.760 ; HA CQ NC 1 115.450 292.880 ; H5 CQ NC 1 115.450 292.880 ; NC CQ NC 1 129.100 585.760 ; HA CR NA 1 120.000 292.880 ; HA CX NA 1 120.000 292.880 ; jtr: HIP HD2-CD2-NE2 HA CR NB 1 120.000 292.880 ; HA CK N* 1 120.000 292.880 ; HA CK NA 1 120.000 292.880 ; wlj HA CK NB 1 120.000 292.880 ; wlj NA CR NA 1 120.000 585.760 ; HISP(OL) NA CR NB 1 120.000 585.760 ; HIS(OL) NA CR CT 1 125.000 585.760 ; wlj NB CR CT 1 125.000 585.760 ; wlj NA CR SY 1 120.000 585.760 ; wlj NB CR SY 1 120.000 585.760 ; wlj C CT CT 1 111.100 527.184 ; AA C_2 CT CT 1 111.100 527.184 ; AA C_3 CT CT 1 111.100 527.184 ; AA C CT CT_2 1 111.100 527.184 ; AA C_2 CT CT_2 1 111.100 527.184 ; AA C_3 CT CT_2 1 111.100 527.184 ; AA C CT_2 CT 1 111.100 527.184 ; AA C_2 CT_2 CT 1 111.100 527.184 ; AA C_3 CT_2 CT 1 111.100 527.184 ; AA CM CT CT 1 111.100 527.184 ; -idem- wlj CW CT HC 1 109.500 292.880 ; jtr: HID HB-CB-CG CV CT HC 1 109.500 292.880 ; jtr: HIE HB-CB-CG CX CT HC 1 109.500 292.880 ; jtr: HIP HB-CB-CG C CT HC 1 109.500 292.880 ; C_2 CT HC 1 109.500 292.880 ; C_3 CT HC 1 109.500 292.880 ; C CT_2 HC 1 109.500 292.880 ; C_2 CT_2 HC 1 109.500 292.880 ; C_3 CT_2 HC 1 109.500 292.880 ; C CT N 1 110.100 527.184 ; AA WORK DONE ON 6/23/82 C_2 CT N 1 110.100 527.184 ; AA WORK DONE ON 6/23/82 C_3 CT N 1 110.100 527.184 ; AA WORK DONE ON 6/23/82 C CT_2 N 1 110.100 527.184 ; AA WORK DONE ON 6/23/82 C_2 CT_2 N 1 110.100 527.184 ; AA WORK DONE ON 6/23/82 C_3 CT_2 N 1 110.100 527.184 ; AA WORK DONE ON 6/23/82 C CT NC 1 110.100 527.184 ; wj C_2 CT NC 1 110.100 527.184 ; wj C_3 CT NC 1 110.100 527.184 ; wj C* CT CT 1 115.600 527.184 ; TRP(OL) C* CT CT_2 1 115.600 527.184 ; TRP(OL) C* CT HC 1 109.500 292.880 ; CS CT CT 1 115.600 527.184 ; wj CS CT HC 1 109.500 292.880 ; wj CA CT CT 1 114.000 527.184 ; PHE(OL) SCH JPC 79,2379 CA CT CT_2 1 114.000 527.184 ; PHE(OL) SCH JPC 79,2379 CA CT HC 1 109.500 292.880 ; CW CT CT 1 114.000 527.184 ; jtr: HID CA-CB-CG CW CT CT_2 1 114.000 527.184 ; jtr: HID CA-CB-CG CV CT CT 1 114.000 527.184 ; jtr: HIE CA-CB-CG CV CT CT_2 1 114.000 527.184 ; jtr: HIE CA-CB-CG CX CT CT 1 114.000 527.184 ; jtr: HIP CA-CB-CG CX CT CT_2 1 114.000 527.184 ; jtr: HIP CA-CB-CG CM CT HC 1 109.500 292.880 ; C= CT HC 1 109.500 292.880 ; wlj CT CT CT 1 112.700 488.273 ; CHARMM 22 parameter file CT_2 CT CT 1 112.700 488.273 ; CHARMM 22 parameter file CT CT_2 CT 1 112.700 488.273 ; CHARMM 22 parameter file CT CT CT_3 1 112.700 488.273 ; CHARMM 22 parameter file C3 CT C3 1 109.500 334.720 ; C3 CT C 1 109.500 527.184 ; from CA-CT-CT CT_2 CT HC 1 110.700 313.800 ; CHARMM 22 parameter file CT CT_2 HC 1 110.700 313.800 ; CHARMM 22 parameter file CT CT HC 1 110.700 313.800 ; CHARMM 22 parameter file CT CT_3 HC 1 110.700 313.800 ; CHARMM 22 parameter file CT_3 CT HC 1 110.700 313.800 ; CHARMM 22 parameter file CT CT_4 HC 1 110.700 313.800 ; Trifluoroethanol CT CT N 1 109.700 669.440 ; ALA JACS 94, 2657 CT CT_2 N 1 109.700 669.440 ; ALA JACS 94, 2657 CT CT_3 N 1 109.700 669.440 ; Pro CD CT CT_3 NT 1 109.700 669.440 ; Pro CD CT CT N* 1 109.500 418.400 ; CT CT N2 1 111.200 669.440 ; ARG JCP 76, 1439 C CT N3 1 111.200 669.440 ; Amino terminal residues C_2 CT N3 1 111.200 669.440 ; Amino terminal residues C_3 CT N3 1 111.200 669.440 ; Amino terminal residues C CT_2 N3 1 111.200 669.440 ; Amino terminal residues C_2 CT_2 N3 1 111.200 669.440 ; Amino terminal residues C_3 CT_2 N3 1 111.200 669.440 ; Amino terminal residues C CT NT 1 111.200 669.440 ; wlj C CT_2 NT 1 111.200 669.440 ; wlj C_2 CT NT 1 111.200 669.440 ; wlj C_3 CT NT 1 111.200 669.440 ; wlj CA CT N 1 109.700 669.440 ; CA CT NT 1 111.200 669.440 ; wlj CA CT NA 1 111.200 669.440 ; wlj CT CT NA 1 111.200 669.440 ; CT CA N 1 109.700 669.440 ; MDDR CT CT N3 1 111.200 669.440 ; LYS(OL) JCP 76, 1439 CT CT_2 N3 1 111.200 669.440 ; LYS(OL) JCP 76, 1439 CT CT_3 N3 1 111.200 669.440 ; CD CT CT OH 1 109.500 418.400 ; CT_2 CT OH 1 109.500 418.400 ; CT CT_4 OH 1 109.500 418.400 ; Trifluoroethanol CA CT OH 1 109.500 418.400 ; wlj CT CT OS 1 109.500 418.400 ; CA CT OS 1 109.500 418.400 ; CT CT S 1 114.700 418.400 ; CYX SCHERAGA JPC 79,1428 CT_2 CT S 1 114.700 418.400 ; CYX SCHERAGA JPC 79,1428 CT CT SH 1 108.600 418.400 ; CYS CT_2 CT SH 1 108.600 418.400 ; CYS CA CT S 1 114.700 418.400 ; wlj CW CT S 1 114.700 418.400 ; wlj CT NT H 1 109.500 292.880 ; CT_3 NT H 1 109.500 292.880 ; CT_2 NT H 1 109.500 292.880 ; CA NT H 1 111.000 292.880 ; wlj/rr anilines CA NT CT 1 109.500 418.400 ; -idem- CT NT CT 1 107.200 433.462 ; wlj - MM3 based JACS 112, 8314 (90) CT NT C3 1 107.200 433.462 ; -idem- C3 NT C3 1 107.200 433.462 ; -idem- HC CT HC 1 107.800 276.144 ; CHARMM 22 parameter file HC CT_2 HC 1 107.800 276.144 ; CHARMM 22 parameter file HC CT_3 HC 1 107.800 276.144 ; CHARMM 22 parameter file HC CT_4 HC 1 107.800 276.144 ; Trifluoroethanol CY CY HC 1 117.200 313.800 ; cyclopropanes - wlj 10/97 CY CY CY 1 60.000 251.040 ; -idem- CY CY CT 1 117.200 313.800 ; -idem- CY CT HC 1 110.700 313.800 ; -idem- HC CY HC 1 114.300 292.880 ; -idem- HC CY CT 1 114.300 292.880 ; -idem- CY CY NC 1 89.000 669.440 ; HC CY NC 1 109.500 292.880 ; small rings HC CY N 1 108.000 292.880 ; -idem- CY CY N 1 126.000 313.800 ; -idem- HC CY S 1 108.000 313.800 ; -idem- CY CY S 1 128.000 460.240 ; -idem- CY N C 1 128.000 460.240 ; -idem- CY N H 1 113.000 334.720 ; -idem- CY S CT 1 94.000 518.816 ; -idem- HC CT N 1 109.500 292.880 ; HC CT_2 N 1 109.500 292.880 ; HC CT_3 N 1 109.500 292.880 ; HC CT_3 NT 1 109.500 292.880 ; HC CT N* 1 109.500 292.880 ; HC CT NA 1 109.500 292.880 ; copy from above for CytH+ (jtr 5-14-91) HC CT N2 1 109.500 292.880 ; HC CT N3 1 109.500 292.880 ; HC CT_2 N3 1 109.500 292.880 ; HC CT_3 N3 1 109.500 292.880 ; HC CT NT 1 109.500 292.880 ; JACS 115, 9620 (93) HC CT_2 NT 1 109.500 292.880 ; HC CT NC 1 109.500 292.880 ; HC CT OH 1 109.500 292.880 ; C CT OH 1 109.500 418.400 ; C_2 CT OH 1 109.500 418.400 ; C_3 CT OH 1 109.500 418.400 ; HC CT_4 OH 1 109.500 292.880 ; fluoroethanol HC CT OS 1 109.500 292.880 ; SUG HC CT S 1 109.500 292.880 ; HC CT P 1 109.500 343.088 ; wlj 11/95 MM3 based JACS 114, 8536 (92) CT CT P 1 109.500 359.824 ; -idem- CA CT P 1 109.500 359.824 ; -idem- CT CT P+ 1 109.500 359.824 ; wlj 9/97 CT P+ CT 1 109.500 376.560 ; -idem- AMBER OS-P-OS HC CT P+ 1 109.500 343.088 ; -idem- HC CT SH 1 109.500 292.880 ; N* CT OS 1 109.500 418.400 ; CW CW NB 1 120.000 585.760 ; HA CV NB 1 120.000 292.880 ; C* CW HA 1 120.000 292.880 ; C* CW NA 1 108.700 585.760 ; TRP(OL) H4 CW NA 1 120.000 292.880 ; HA CA NA 1 120.000 292.880 ; C N C3 1 121.900 418.400 ; C N CT 1 121.900 418.400 ; C N CT_2 1 121.900 418.400 ; C N CT_3 1 121.900 418.400 ; C N CA 1 121.900 418.400 ; wlj C N H 1 119.800 292.880 ; AA(OL) C3 N H 1 118.400 317.984 ; CT N CT 1 118.000 418.400 ; PRO(OL) DETAR JACS 99,1232 CT_2 N CT 1 118.000 418.400 ; PRO(OL) DETAR JACS 99,1232 CT_2 N CT_2 1 118.000 418.400 ; PRO(OL) DETAR JACS 99,1232 CT_3 N CT 1 118.000 418.400 ; PRO(OL) DETAR JACS 99,1232 CT_3 N CT_2 1 118.000 418.400 ; PRO(OL) DETAR JACS 99,1232 CT_3 NT CT_2 1 118.000 418.400 ; PRO(OL) DETAR JACS 99,1232 CA N CT 1 118.000 418.400 ; wj CA NC CT 1 118.000 418.400 ; wj CT N H 1 118.400 317.984 ; CT_2 N H 1 118.400 317.984 ; CT_3 N H 1 118.400 317.984 ; CT_3 N H3 1 118.400 317.984 ; H N H 1 120.000 292.880 ; ADE,CYT,GUA,GLN,ASN ** H N2 H 1 113.000 292.880 ; wlj H3 N H3 1 120.000 292.880 ; ADE,CYT,GUA,GLN,ASN ** C N* CM 1 121.600 585.760 ; C_2 N* CM 1 121.600 585.760 ; C_3 N* CM 1 121.600 585.760 ; C NA CM 1 121.600 585.760 ; copy from above for CytH+ (jtr 5-14-91) C_2 NA CM 1 121.600 585.760 ; copy from above for CytH+ (jtr 5-14-91) C_3 NA CM 1 121.600 585.760 ; copy from above for CytH+ (jtr 5-14-91) C N* CT 1 117.600 585.760 ; C_2 N* CT 1 117.600 585.760 ; C_3 N* CT 1 117.600 585.760 ; C N* H 1 119.200 292.880 ; C_2 N* H 1 119.200 292.880 ; C_3 N* H 1 119.200 292.880 ; C3 N* CB 1 125.800 585.760 ; 9 methylated guan,aden C3 N* CK 1 128.800 585.760 ; CM N* CT 1 121.200 585.760 ; CM N* H 1 119.200 292.880 ; CM NA H 1 119.200 292.880 ; copy from above for CytH+ (jtr 5-14-91) C3 N2 CA 1 123.200 418.400 ; ARG(OL) CA N2 CA 1 123.200 418.400 ; CA N2 CT 1 123.200 418.400 ; ARG(OL) CA N2 CX 1 123.200 418.400 ; N2 CX NZ 1 180.000 585.760 ; CA N2 H 1 120.000 292.880 ; ARG(OL) CQ N2 H 1 120.000 292.880 ; wlj CA N2 H3 1 120.000 292.880 ; ADE,CYT,GUA,ARG CT N2 H3 1 118.400 292.880 ; ARG(OL) CT N2 H 1 118.400 292.880 ; H3 N2 H3 1 120.000 292.880 ; ADE,CYT,GUA,GLN,ASN,ARG C3 N3 H3 1 109.500 292.880 ; CT N3 H3 1 109.500 292.880 ; LYS CT_2 N3 H3 1 109.500 292.880 ; LYS CT N3 H 1 109.500 292.880 ; LYS CT_3 N3 H3 1 109.500 292.880 ; Pro CD CT_3 N3 H 1 109.500 292.880 ; Pro CD H3 N3 H3 1 109.500 292.880 ; LYS H N3 H 1 109.500 292.880 ; LYS CT N3 CT 1 113.000 418.400 ; proline j.phys chem 1979 p 2361 CT_2 N3 CT_3 1 113.000 418.400 ; proline j.phys chem 1979 p 2361 CT_2 N3 CT 1 113.000 418.400 ; proline j.phys chem 1979 p 2361 C NA C 1 126.400 585.760 ; URA C NA C_2 1 126.400 585.760 ; URA C NA C_3 1 126.400 585.760 ; URA C_2 NA C_2 1 126.400 585.760 ; URA C_2 NA C_3 1 126.400 585.760 ; URA C_3 NA C_3 1 126.400 585.760 ; URA C N C 1 126.400 585.760 ; wlj C NA CA 1 125.200 585.760 ; GUA C_2 NA CA 1 125.200 585.760 ; GUA C_3 NA CA 1 125.200 585.760 ; GUA C N CQ 1 125.200 585.760 ; wj C NA H 1 116.800 292.880 ; GUA,URA(2) C_2 NA H 1 116.800 292.880 ; GUA,URA(2) C_3 NA H 1 116.800 292.880 ; GUA,URA(2) CA NA H 1 118.000 292.880 ; GUA CQ N H 1 118.000 292.880 ; wlj CN NA CW 1 111.600 585.760 ; TRP(OL) CN NA H 1 123.100 292.880 ; TRP CR NA H 1 120.000 292.880 ; HIS(OL) CW NA H 1 120.000 292.880 ; HIS(OL) CX NA H 1 120.000 292.880 ; jtr HIP CB N* CK 1 105.400 585.760 ; CB N* CT 1 125.800 585.760 ; CB N* H 1 125.800 251.040 ; CK N* CT 1 128.800 585.760 ; CK N* H 1 128.800 251.040 ; CB NA CK 1 105.400 585.760 ; wlj CB NA CT 1 125.800 585.760 ; wlj CB NA H 1 125.800 251.040 ; wlj CK NA CT 1 128.800 585.760 ; wlj CK NA H 1 128.800 251.040 ; wlj CB NB CK 1 103.800 585.760 ; CR NB CV 1 110.000 585.760 ; HIS(OL) wlj 1/97 CR NB CB 1 110.000 585.760 ; wlj CR NB CW 1 110.000 585.760 ; C NC CA 1 120.500 585.760 ; CYT C_2 NC CA 1 120.500 585.760 ; CYT C_3 NC CA 1 120.500 585.760 ; CYT CA NC CB 1 112.200 585.760 ; GUA CA NC CQ 1 118.600 585.760 ; CQ NC CQ 1 118.600 585.760 ; wlj 1,3,5-triazine CB NC CQ 1 111.000 585.760 ; CR NC CQ 1 111.000 585.760 ; wj C3 NT H 1 108.100 361.498 ; wlj MM3 based H NT H 1 106.400 364.845 ; wlj MM3 based H N OH 1 110.200 292.880 ; wlj C N OH 1 115.700 384.928 ; wlj N OH HO 1 105.400 410.032 ; wlj C OH HO 1 113.000 292.880 ; TYR(PHENOL) HARMONY MEOH CA OH HO 1 113.000 292.880 ; CM OH HO 1 109.000 292.880 ; wj C3 OH HO 1 108.500 460.240 ; SUG,SER(OL,mod) CT OH HO 1 108.500 460.240 ; CT_4 OH HO 1 108.500 460.240 ; Trifluoroethanol HO OH P 1 108.500 376.560 ; SUG(OL) C OS C3 1 116.900 694.544 ; C_2 OS C3 1 116.900 694.544 ; O C OS 1 123.400 694.544 ; J.Comp.Chem.1990,11,1181 for SKF8 O C_2 OS 1 123.400 694.544 ; J.Comp.Chem.1990,11,1181 for SKF8 O_2 C_2 OS 1 123.400 694.544 ; J.Comp.Chem.1990,11,1181 for SKF8 C OS CT 1 116.900 694.544 ; -idem- C_2 OS CT 1 116.900 694.544 ; -idem- OS C CT 1 111.400 677.808 ; -idem- OS C_2 CT 1 111.400 677.808 ; -idem- OS C CT_2 1 111.400 677.808 ; -idem- OS C CA 1 111.400 677.808 ; wlj C OS CA 1 116.900 694.544 ; wlj C_2 OS CA 1 116.900 694.544 ; wlj OS CO OH 1 111.550 774.876 ; Ha,CarbRes 180,207(88)Merz,JCC 15,1019 (94) OS CO OS 1 111.550 774.876 ; ACETAL- wlj 2/93 C3 OS CO 1 113.000 836.800 ; -idem- C3 CO OS 1 109.500 669.440 ; -idem- C3 CO C3 1 109.500 334.720 ; -idem- OS CO CT 1 109.500 418.400 ; hexopyranoses : CT-CT-OS- wd 3/95 Glucose CO CT CT 1 112.700 488.273 ; -idem- : CT-CT-CT- wd 6/95 Glucose CT CO OH 1 109.500 418.400 ; -idem- : CT-CT-OH- wd 6/95 Glucose CT CO HC 1 110.700 313.800 ; -idem- : CT-CT-HC- wd 6/95 Glucose CO OH HO 1 108.500 460.240 ; -idem- : CT-OH-HO- wd 6/95 Glucose OS CO HC 1 109.500 292.880 ; -idem- : HC-CT-OS- wd 6/95 Glucose CO OS CT 1 109.500 502.080 ; -idem- : CT-OS-CT- wd 6/95 Glucose CO CT HC 1 110.700 313.800 ; -idem- : CT-CT-HC- wd 6/95 Glucose CO CT OH 1 109.500 418.400 ; -idem- : CT-CT-OH- wd 6/95 Glucose OH CO HC 1 109.500 292.880 ; -idem- : HC-CT-OS- wd 6/95 Glucose HC CO HC 1 109.500 276.144 ; -idem- : HC-CT-HC- wd 6/95 CA OS NB 1 108.900 585.760 ; CA OS CA 1 111.000 627.600 ; wlj 9/97 CA OS P 1 120.500 836.800 ; mll C3 OS P 1 120.500 836.800 ; DMPhos based CT OS CT 1 109.500 502.080 ; CT OS CA 1 111.000 627.600 ; wlj 9/97 CT OS CM 1 111.000 627.600 ; wlj CT OS P 1 120.500 836.800 ; O2 P O2 1 119.900 1171.520 ; SUG(OL) O2 P OH 1 108.230 376.560 ; SUG(OL) O2 P OS 1 108.230 836.800 ; SUG(OL) OH P OS 1 102.600 376.560 ; SUG(OL) OS P OS 1 102.600 376.560 ; SUG(OL) O P OH 1 108.230 836.800 ; SUG(OL) O P OS 1 108.230 836.800 ; SUG(OL) OH P OH 1 102.600 376.560 ; SUG(OL) CT P OS 1 109.500 376.560 ; wlj 11/95 CT P O2 1 109.500 376.560 ; wlj 11/95 CT P O 1 109.500 376.560 ; wlj 11/95 CA P OS 1 109.500 376.560 ; wlj 11/95 CA P OH 1 109.500 376.560 ; wlj 11/95 CA P O 1 109.500 376.560 ; wlj 11/95 C3 S LP 1 96.700 1255.200 ; C3 S S 1 103.700 569.024 ; CYX(OL) SCHERAGA JPC 79,1428 CT S CT 1 98.900 518.816 ; MET(OL) CR S CW 1 90.000 619.232 ; wlj CW S CW 1 97.000 619.232 ; wlj CT S LP 1 96.700 1255.200 ; CT S S 1 103.700 569.024 ; CYX(OL) SCHERAGA JPC 79,1428 LP S LP 1 160.000 0.000 ; LP S S 1 96.700 1255.200 ; C3 SH HS 1 96.000 368.192 ; CYS(OL) C3 SH LP 1 96.700 1255.200 ; CT SH HS 1 96.000 368.192 ; CYS(OL) CA SH HS 1 96.000 418.400 ; wlj CT SH LP 1 96.700 1255.200 ; HS SH HS 1 92.070 292.880 ; HS SH LP 1 96.700 1255.200 ; LP SH LP 1 160.000 0.000 ; P OS P 1 120.500 836.800 ; CA CT CA 1 109.500 334.720 ; -idem- CA CT C 1 112.000 527.184 ; wlj CA CT C_2 1 112.000 527.184 ; wlj CA CT C_3 1 112.000 527.184 ; wlj CT CA NA 1 120.000 585.760 ; Added DSM (from CT-CC-NA) CT CA N2 1 120.100 585.760 ; N2 CA N 1 120.000 585.760 ; CA NA CA 1 125.200 585.760 ; Added DSM (from C-NA-CA) CA CA NB 1 108.700 585.760 ; Added DSM (from CA-CA-NA) NA CA NB 1 123.300 585.760 ; Added DSM (from NA-CA-NC) CA NB CA 1 125.200 585.760 ; Added DSM (from C-NA-CA) HA CA NB 1 119.100 292.880 ; Added DSM (from HC-CM-NA) CA CA N 1 120.000 585.760 ; Added DSM (from CA-CA-NA) CA N H 1 119.800 292.880 ; Added DSM (from C-N-H) CB CT HC 1 109.500 292.880 ; Added DSM (from CA-CT-HC) CA CB CT 1 120.000 585.760 ; Added DSM (from CA-CA-CT) CB CA NA 1 108.700 585.760 ; Added DSM (from CA-CA-NA) CB CB CT 1 120.000 585.760 ; Added DSM (from CA-CA-CT) CB CB NB 1 110.400 585.760 ; GUA,ADE CB CT CT 1 114.000 527.184 ; Added DSM (from CA-CT-CT) CT CT F 1 109.500 418.400 ; PAK F-CT-HC (emd 5-09-94) CT_4 CT F 1 109.500 418.400 ; Trifluoroethanol CA CT F 1 109.500 418.400 ; wlj F CT F 1 109.100 644.336 ; PAK F-CT-F (emd 5-09-94) HC CT F 1 107.000 334.720 ; wlj CT C C 1 117.200 669.440 ; (JP 1-6-91) SKF8 CT C C_2 1 117.200 669.440 ; (JP 1-6-91) SKF8 CT C C_3 1 117.200 669.440 ; (JP 1-6-91) SKF8 CT C_2 C 1 117.200 669.440 ; (JP 1-6-91) SKF8 CT C_2 C_2 1 117.200 669.440 ; (JP 1-6-91) SKF8 CT C_2 C_3 1 117.200 669.440 ; (JP 1-6-91) SKF8 C C O 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C C O_2 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C C O_3 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C C_2 O_2 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C_2 C O 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C_2 C O_2 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C_2 C O_3 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C_2 C_2 O_2 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C_3 C O 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C_3 C O_2 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C_3 C O_3 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C_3 C_2 O_2 1 121.400 669.440 ; ketone (JP 1-5-91) SKF8 C C N 1 116.600 585.760 ; (JP 1-5-91) SKF8 C_2 C N 1 116.600 585.760 ; (JP 1-5-91) SKF8 C_3 C N 1 116.600 585.760 ; (JP 1-5-91) SKF8 C C_2 N 1 116.600 585.760 ; (JP 1-5-91) SKF8 C_2 C_2 N 1 116.600 585.760 ; (JP 1-5-91) SKF8 C_3 C_2 N 1 116.600 585.760 ; (JP 1-5-91) SKF8 OY SY N 1 107.000 1004.160 ; OY SY OY 1 119.000 870.272 ; OY SZ CT 1 107.000 619.232 ; OY SY CT 1 108.900 619.232 ; OY SY CA 1 107.200 619.232 ; N SY CA 1 103.000 836.800 ; SY CA CA 1 119.400 711.280 ; SY CT HC 1 109.500 292.880 ; SZ CT HC 1 109.500 292.880 ; CT SY CT 1 102.000 518.816 ; CA SY CT 1 102.000 518.816 ; CR SY CT 1 102.000 518.816 ; CU CT SY 1 119.400 711.280 ; CT SZ CT 1 96.000 518.816 ; CT CT SY 1 108.600 418.400 ; CT CT SZ 1 108.600 418.400 ; N SY CT 1 103.000 836.800 ; SY N CT 1 120.000 418.400 ; H N SY 1 111.000 836.800 ; OS C N 1 111.400 677.808 ; bhap, copy from OS-C-CT rcr HIVRT OS C_2 N 1 111.400 677.808 ; bhap, copy from OS-C-CT rcr HIVRT CT NT SY 1 108.600 418.400 ; bhap, copy from CT-CT-SY rcr HIVRT C CT F 1 109.500 418.400 ; bhap, copy from CT-CT-F rcr HIVRT C_2 CT F 1 109.500 418.400 ; bhap, copy from CT-CT-F rcr HIVRT C_3 CT F 1 109.500 418.400 ; bhap, copy from CT-CT-F rcr HIVRT SY CT F 1 109.500 418.400 ; bhap, copy from CT-CT-F rcr HIVRT SY NT H 1 115.000 292.880 ; bhap, adjusted from CT-NT-H rcr HIVRT C CW NA 1 120.000 711.280 ; bhap, copy from C-CA-CA rcr HIVRT C_2 CW NA 1 120.000 711.280 ; bhap, copy from C-CA-CA rcr HIVRT C_3 CW NA 1 120.000 711.280 ; bhap, copy from C-CA-CA rcr HIVRT NT C CW 1 116.000 585.760 ; bhap, copy from CT-C-CT rcr HIVRT C CW CS 1 120.000 711.280 ; bhap, copy from C-CA-CA rcr HIVRT C_2 CW CS 1 120.000 711.280 ; bhap, copy from C-CA-CA rcr HIVRT C_3 CW CS 1 120.000 711.280 ; bhap, copy from C-CA-CA rcr HIVRT CB CS HA 1 120.000 292.880 ; bhap, copy from CB-CA-HA rcr HIVRT CW C O 1 120.400 669.440 ; bhap, copy from CA-C-O rcr HIVRT CW C O_2 1 120.400 669.440 ; bhap, copy from CA-C-O rcr HIVRT CW C O_3 1 120.400 669.440 ; bhap, copy from CA-C-O rcr HIVRT CW C_2 O_2 1 120.400 669.440 ; bhap, copy from CA-C-O rcr HIVRT C NT CT 1 111.100 527.184 ; bhap, copy from C-CT-CT rcr HIVRT C_2 NT CT 1 111.100 527.184 ; bhap, copy from C-CT-CT rcr HIVRT C_3 NT CT 1 111.100 527.184 ; bhap, copy from C-CT-CT rcr HIVRT C CT C 1 111.100 527.184 ; lac, copy from C-CT-CT rcr HIVRT C_2 CT C 1 111.100 527.184 ; lac, copy from C-CT-CT rcr HIVRT C_3 CT C 1 111.100 527.184 ; lac, copy from C-CT-CT rcr HIVRT C CT OS 1 109.500 418.400 ; lac, copy from CT-CT-OS rcr HIVRT C_2 CT OS 1 109.500 418.400 ; lac, copy from CT-CT-OS rcr HIVRT C_3 CT OS 1 109.500 418.400 ; lac, copy from CT-CT-OS rcr HIVRT N CT OS 1 109.500 418.400 ; lac, copy from CT-CT-OS rcr HIVRT NT C O 1 120.400 669.440 ; nev, copy from CT-C-O rcr HIVRT NT C O_2 1 120.400 669.440 ; nev, copy from CT-C-O rcr HIVRT NT C O_3 1 120.400 669.440 ; nev, copy from CT-C-O rcr HIVRT NT C_2 O_2 1 120.400 669.440 ; nev, copy from CT-C-O rcr HIVRT NT C CT 1 116.000 585.760 ; nev, copy from CT-C-CT rcr HIVRT NT C_2 CT 1 116.000 585.760 ; nev, copy from CT-C-CT rcr HIVRT CA NT C 1 112.000 527.184 ; nev, copy from CA-CT-C rcr HIVRT CA NT C_2 1 112.000 527.184 ; nev, copy from CA-CT-C rcr HIVRT CA NT C_3 1 112.000 527.184 ; nev, copy from CA-CT-C rcr HIVRT CA NT SY 1 108.600 418.400 ; nev, copy from CT-CT-SY rcr HIVRT OY SY NT 1 108.900 619.232 ; nev, copy from OY-SY-CT rcr HIVRT NT SY CT 1 102.000 518.816 ; nev, copy from CT-SY-CT rcr HIVRT NT CT S 1 114.700 418.400 ; nev, copy from CT-CT-S rcr HIVRT HC CY NT 1 114.300 292.880 ; nev, copy from HC-CY-CT rcr HIVRT CY CY NT 1 117.200 313.800 ; nev, copy from CY-CY-CT rcr HIVRT CA NT CY 1 109.500 418.400 ; nev, copy from CA-NT-CT rcr HIVRT NC CA Cl 1 120.000 627.600 ; nev, copy from CA-CA-Cl rcr HIVRT CA NT CA 1 109.500 334.720 ; nev, copy from CA-CT-CA rcr HIVRT NC CA NT 1 116.000 585.760 ; nev, copy from NC-CA-CT rcr HIVRT CM CM CY 1 124.000 585.760 ; hept, copy from CM-CM-CT rcr HIVRT CM CY HC 1 109.500 292.880 ; hept, copy from CM-CT-HC rcr HIVRT CM CY CY 1 114.000 527.184 ; hept, copy from CA-CT-CT rcr HIVRT C CM CY 1 119.700 585.760 ; hept, copy from C-CM-CT rcr HIVRT C_2 CM CY 1 119.700 585.760 ; hept, copy from C-CM-CT rcr HIVRT C_3 CM CY 1 119.700 585.760 ; hept, copy from C-CM-CT rcr HIVRT N* CM CT 1 120.000 585.760 ; hept, copy from PHE(OL) rcr HIVRT NA CM CT 1 120.000 585.760 ; hept, copy from PHE(OL) rcr HIVRT S CM CM 1 119.400 711.280 ; hept, copy from SY-CA-CA rcr HIVRT S CM N* 1 119.400 711.280 ; hept, copy from SY-CA-CA rcr HIVRT S CM NA 1 119.400 711.280 ; hept, copy from SY-CA-CA rcr HIVRT N* CM OS 1 120.000 585.760 ; hept, copy from CA-CA-OS rcr HIVRT NA CM OS 1 120.000 585.760 ; hept, copy from CA-CA-OS rcr HIVRT CA S CM 1 104.200 518.816 ; hept, adjusted from CT-S-CT rcr HIVRT CM OS CA 1 111.000 627.600 ; hept, copy from CT-S-CT rcr HIVRT CM CT CA 1 109.500 334.720 ; hept, copy from CA-CT-CA rcr HIVRT S CA CA 1 119.400 711.280 ; thioanisole copy from SY-CA-CA rcr HIVRT P CA CA 1 119.400 711.280 ; CA S CT 1 104.200 518.816 ; thioanisole adjusted from CT-S-CT rcr HIVRT ; Charged Glutamine ; See. Patriksson et al. Int. J. Mass. Spectrom. 248 pp 124-135 (2006) OH C N 1 115.43 292.88 [ dihedraltypes ] ; i j k l func coefficients ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form ; according to the formula in the Gromacs manual. Br C CB CT 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; acyl halide Br C CT HC 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ; acyl halide Br CT CT Br 3 -0.52300 0.52300 0.00000 0.00000 0.00000 0.00000 ; dichloride Br CT CT CT 3 0.83680 2.51040 0.00000 -3.34720 0.00000 0.00000 ; alkyl bromide Br CT CT HC 3 0.83680 2.51040 0.00000 -3.34720 0.00000 0.00000 ; alkyl bromide C C N H 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) C C N CT 3 21.33840 -0.83680 -20.50160 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) C C CT HC 3 0.17782 0.53346 0.00000 -0.71128 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) C C OH HO 3 29.28800 -6.27600 -23.01200 0.00000 0.00000 0.00000 ; oxalic acid, etc. C N C N 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; imides C N CT CA 3 -4.70700 2.92044 1.78656 0.00000 0.00000 0.00000 ; from N-ethylformamide C N CT CT 3 -4.70700 2.92044 1.78656 0.00000 0.00000 0.00000 ; N-ethylformamide C N CT HC 3 -0.29079 -0.87237 0.00000 1.16315 0.00000 0.00000 ; N-methylformamide C N CY CY 3 -4.70700 2.92044 1.78656 0.00000 0.00000 0.00000 ; small ring C N CY HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; small ring C N OH HO 3 -15.27160 -7.89939 28.03280 -4.86181 0.00000 0.00000 ; hydroxamic acids C N CT_3 CT 3 15.70255 31.75656 -3.66936 -43.78975 0.00000 0.00000 ; Phi prime peptides AA C N CT_3 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; C N CT_2 CT 3 15.70255 31.75656 -3.66936 -43.78975 0.00000 0.00000 ; Phi prime peptides AA C N CT_2 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; Phi bis peptides AA C CT N C 3 -10.35749 -29.58716 -1.16734 41.11199 0.00000 0.00000 ; Phi peptides AA C(O)-N-Ca-C(O) C_3 CT N C 3 -10.35749 -29.58716 -1.16734 41.11199 0.00000 0.00000 ; Phi peptides AA C(O)-N-Ca-C(O) C CT N CT 3 -5.72371 -18.33847 -5.23419 29.29636 0.00000 0.00000 ; from Pro (fit to AM1) CD-N-CA-C C CT CT C* 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; C CT CT CA 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; aldehyde & ketone & acyl halide C CT CT CT 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; butanamide C CT CT HC 3 -0.20920 -0.62760 0.00000 0.83680 0.00000 0.00000 ; C CT CT_2 HC 3 -0.15899 -0.47698 0.00000 0.63596 0.00000 0.00000 ; C_3 CT CT_2 HC 3 -0.15899 -0.47698 0.00000 0.63596 0.00000 0.00000 ; C CT CT_2 C 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; C CT NT H 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; amine all-atom C CT_2 NT H 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; aa H2N-terminus C CT OH HO 3 -0.44350 3.83255 0.72801 -4.11705 0.00000 0.00000 ; C CT N3 H3 3 0.72592 2.17777 0.00000 -2.90370 0.00000 0.00000 ; ammonium ion all-atom C NC OH HO 3 18.82800 -6.27600 -12.55200 0.00000 0.00000 0.00000 ; oxime B3LYP/6-31G* C NC OS CT 3 18.82800 -6.27600 -12.55200 0.00000 0.00000 0.00000 ; oxime 11/00 C OS CA CA 3 10.46000 0.00000 -10.46000 0.00000 0.00000 0.00000 ; phenyl acetate C OS CT CT 3 -2.19660 5.20071 0.52719 -3.53130 0.00000 0.00000 ; esters C OS CT HC 3 0.41421 1.24265 0.00000 -1.65686 0.00000 0.00000 ; esters C CT_2 N C 3 -10.35749 -29.58716 -1.16734 41.11199 0.00000 0.00000 ; Phi peptides AA C(O)-N-Ca-C(O) C_3 CT_2 N C 3 -10.35749 -29.58716 -1.16734 41.11199 0.00000 0.00000 ; C-term phi. C CT_2 N H 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides H-N-CA-X C CT_2 N CT_3 3 -5.72371 -18.33847 -5.23419 29.29636 0.00000 0.00000 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97 C CT_2 NT CT_3 3 -5.72371 -18.33847 -5.23419 29.29636 0.00000 0.00000 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97 C_3 CT_2 N CT_3 3 -5.72371 -18.33847 -5.23419 29.29636 0.00000 0.00000 ; Pro COO- terminus. C_3 CT_2 NT CT_3 3 -5.72371 -18.33847 -5.23419 29.29636 0.00000 0.00000 ; Pro COO- terminus. C CT CT CT_2 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; GLUH C CT_2 CT S 3 -16.25902 9.08765 7.17138 0.00000 0.00000 0.00000 ; Chi for Cyx (Cystine) C CT_2 CT C* 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; aldehyde & ketone C CT_2 CT C_3 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; aldehyde & ketone C CT_2 CT CA 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; peptide, aldehyde & ketone C CT_2 CT CT 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; peptide, aldehyde & ketone C CT_2 CT CV 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; peptide, aldehyde & ketone C CT_2 CT CW 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; peptide, aldehyde & ketone C CT_2 CT CX 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; peptide, aldehyde & ketone C CT_2 CT HC 3 -0.15899 -0.47698 0.00000 0.63596 0.00000 0.00000 ; peptide, aldehyde & ketone C CT_2 CT OH 3 -15.47661 11.82816 3.64845 0.00000 0.00000 0.00000 ; Chi for Ser & Thr C_3 CT_2 CT OH 3 -15.47661 11.82816 3.64845 0.00000 0.00000 0.00000 ; C-terminal Chi for Ser & Thr C CT_2 CT SH 3 -16.25902 9.08765 7.17138 0.00000 0.00000 0.00000 ; Chi for Cys (Cysteine) C CT_2 N3 H3 3 0.72592 2.17777 0.00000 -2.90370 0.00000 0.00000 ; peptides H-N-CA-C C_3 CT_2 N3 H3 3 0.72592 2.17777 0.00000 -2.90370 0.00000 0.00000 ; Zwitterion AAs C CT_2 N3 CT_3 3 -5.72371 -18.33847 -5.23419 29.29636 0.00000 0.00000 ; C CT_2 NT CT_3 3 -5.72371 -18.33847 -5.23419 29.29636 0.00000 0.00000 ; C* CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; aromatics C* CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA C* CT CT_2 HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; C* CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA C* CW NA H 3 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 ; TRP chi-4 C* CW NA CN 3 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 ; TRP chi-4 C3 CT OH HO 3 0.41840 1.25520 0.00000 -1.67360 0.00000 0.00000 ; Alcohols with scl14 = 2,2 C= CM CA CA 3 16.02681 -4.39111 -14.02895 2.39325 0.00000 0.00000 ; styrene C= CM CT CT 3 0.52719 -6.39734 -1.69452 7.56467 0.00000 0.00000 ; alkenes C= CM OS CT 3 5.23000 7.32200 -12.55200 0.00000 0.00000 0.00000 ; vinyl ether C= CT OH HO 3 -1.88280 1.88280 0.00000 0.00000 0.00000 0.00000 ; allyl alcohols CA C OH HO 3 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ; benzoic acids & esters CA C OS CT 3 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ; benzoic acids & esters CA N C O 3 25.47638 0.00000 -25.47638 0.00000 0.00000 0.00000 ; amides O-C(O)-N-C CA N C CT 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; amides - V1 changed to 2.3 CA N CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; tertiary amide CA S CT HC 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; sulfide all-atom CA CA C N 3 4.60240 0.00000 -4.60240 0.00000 0.00000 0.00000 ; aryl amides, benzamides CA CA C O 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; aryl acid, amide, ester CA CA C CT 3 0.83680 0.00000 -0.83680 0.00000 0.00000 0.00000 ; aryl ketone CA CA C HC 3 0.83680 0.00000 -0.83680 0.00000 0.00000 0.00000 ; aryl aldehyde CA CA C OH 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; aryl acid, ester CA CA C OS 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; aryl acid, amide, ester CA CA C O_2 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; aryl acid, amide, ester CA CA C O_3 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; aryl acid, amide, ester CA CA S CT 3 2.51040 0.00000 -2.51040 0.00000 0.00000 0.00000 ; thioanisole fit to MP4 CA CA CA N2 3 0.00000 0.00000 16.73600 0.00000 -16.73600 0.00000 ; benzamidine CA CA CM CM 3 16.02681 -4.39111 -14.02895 2.39325 0.00000 0.00000 ; styrene CA CA CM CT 3 -1.79284 -0.42886 2.22170 0.00000 0.00000 0.00000 ; 1-methylstyrene CA CA CT F 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; fluoromethyl benzene CA CA CT CT 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; ethyl benzene CA CA CT Cl 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; chloromethyl benzene CA CA CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; ethyl benzene CA CA N2 H 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline CA CA N2 H3 3 5.85760 0.00000 -5.85760 0.00000 0.00000 0.00000 ; from aniline CA CA NO ON 3 4.81160 0.00000 -4.81160 0.00000 0.00000 0.00000 ; CA-CA-NO-ON nitrobenzene CA CA NT H 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline CA CA NT CT 3 5.18398 35.93219 -14.35530 -26.76086 0.00000 0.00000 ; substituted-aniline CA CA OH HO 3 7.03749 0.00000 -7.03749 0.00000 0.00000 0.00000 ; phenol all-atom CA CA OS P 3 12.51016 0.00000 -12.51016 0.00000 0.00000 0.00000 ; PhOPO3 (2-) mll CT CT OS P 3 12.51016 0.00000 -12.51016 0.00000 0.00000 0.00000 ; Guess for phosphate in lipids N3 CT CT OS 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; Guess for lipids CA CA OS CT 3 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 ; anisole CA CA OS C_2 3 10.46000 0.00000 -10.46000 0.00000 0.00000 0.00000 ; phenyl acetate CA CA SH HS 3 4.60240 0.00000 -4.60240 0.00000 0.00000 0.00000 ; aromatic thiol CA CA SY N 3 0.00628 -4.19864 3.21331 0.97905 0.00000 0.00000 ; sulfonamide CA CA SY2 CT 3 -3.76560 0.00000 3.76560 0.00000 0.00000 0.00000 ; sulfone 10/00 B3LYP PhSO2Me CA CA C_2 CT 3 0.83680 0.00000 -0.83680 0.00000 0.00000 0.00000 ; aryl ketone CA CA C_2 HC 3 0.83680 0.00000 -0.83680 0.00000 0.00000 0.00000 ; aryl aldehyde CA CT C O 3 2.28446 0.00000 -2.28446 0.00000 0.00000 0.00000 ; RCOOH acid CA CT C O_3 3 2.28446 0.00000 -2.28446 0.00000 0.00000 0.00000 ; RCOOH acid CT CT N CT 3 -8.97677 -76.68644 -8.61067 94.27389 0.00000 0.00000 ; from Pro CG-CD-N-CA CA CT N CT 3 -8.97677 -76.68644 -8.61067 94.27389 0.00000 0.00000 ; from Pro CG-CD-N-CA CA CT P O2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; phosphonates CA CT P OS 3 4.70700 -4.70700 0.00000 0.00000 0.00000 0.00000 ; phosphonates CA CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; sulfide all-atom CA CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; CA CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; ethyl benzene CA CT CT_2 HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; ethyl benzene CA CT CT N3 3 2.09200 -2.09200 0.00000 0.00000 0.00000 0.00000 ; phenethylammonium - JACS 119,12292(97) CA CT CT NC 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; CA CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; amine all-atom CA CT CT_2 NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; AA H2N-terminus. CA CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; from alcohol CA CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; alcohols, ethers AA CA CT CT C_2 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; aldehyde & ketone CA CT N2 CA 3 3.80117 -6.95172 -1.01671 4.16726 0.00000 0.00000 ; ethylguanidinium ion CA CT NT CT 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; amine all-atom CA CT OH HO 3 -1.88280 1.88280 0.00000 0.00000 0.00000 0.00000 ; benzyl alcohols CA CT OS CO 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; CA CT OS CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; ethers AA CA CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CA CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CA N2 CA N2 3 33.20422 0.00000 -33.20422 0.00000 0.00000 0.00000 ; methylguanidinium ion CA N2 CA NC 3 33.20422 0.00000 -33.20422 0.00000 0.00000 0.00000 ; CA N2 CT CT 3 3.80117 -6.95172 -1.01671 4.16726 0.00000 0.00000 ; ethylguanidinium ion CA NY CT CT 3 3.80117 -6.95172 -1.01671 4.16726 0.00000 0.00000 ; ARGN. CA N2 CT HC 3 0.37028 1.11086 0.00000 -1.48114 0.00000 0.00000 ; methylguanidinium ion CA NY CT HC 3 0.37028 1.11086 0.00000 -1.48114 0.00000 0.00000 ; ARGN CA NC CT CT 3 3.80117 -6.95172 -1.01671 4.16726 0.00000 0.00000 ; CA NT CT HC 3 1.17152 3.51456 0.00000 -4.68608 0.00000 0.00000 ; amine all-atom CA OS C O 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ; phenyl acetate CA OS C CT 3 24.05800 -3.13800 -20.92000 0.00000 0.00000 0.00000 ; phenyl acetate CA OS P O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; phosphonates CA OS CT CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; ethers AA CA OS CT CA 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; ethers AA CA OS CT HC 3 1.58992 4.76976 0.00000 -6.35968 0.00000 0.00000 ; ethers AA CA SY N H 3 -15.61050 0.70291 20.50579 -5.59819 0.00000 0.00000 ; sulfonamide CA SY N CT 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; sulfonamide CA SY2 CT HC 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; sulfone CB C* CT CT 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; 3-ethylindole CB C* CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; 3-methylindole CB C* CT CT_2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CB CA CT CT 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; ethyl benzene CB CA CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; ethyl benzene CB CA N2 H 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline-like CB CS CT CT 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; 3-ethylindole CB CS CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; 3-methylindole CK CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; aromatics CK N* CT CT 3 -3.55640 2.09200 1.46440 0.00000 0.00000 0.00000 ; imidazoles, indoles, purines CK N* CT OS 3 -9.41400 3.13800 6.27600 0.00000 0.00000 0.00000 ; imidazoles, indoles, purines CK NA CT CT 3 -3.55640 2.09200 1.46440 0.00000 0.00000 0.00000 ; imidazoles, indoles, purines CK NA CT OS 3 -9.41400 3.13800 6.27600 0.00000 0.00000 0.00000 ; imidazoles, indoles, purines CM C N H 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; amides CM N C O 3 25.47638 0.00000 -25.47638 0.00000 0.00000 0.00000 ; amides CM C= C O 3 30.33400 -5.23000 -25.10400 0.00000 0.00000 0.00000 ; acrolein CM C= C CT 3 -10.87840 -1.67360 12.55200 0.00000 0.00000 0.00000 ; methyl vinyl ketone CM C= C OH 3 -5.85760 -6.69440 12.55200 0.00000 0.00000 0.00000 ; acrylic acid CM C= C= CM 3 21.73797 2.40789 -16.96612 -7.17975 0.00000 0.00000 ; diene C=C-C=C CM C= C= CT 3 -0.77822 -2.33467 0.00000 3.11290 0.00000 0.00000 ; diene - generic CM C= C= HC 3 -0.77822 -2.33467 0.00000 3.11290 0.00000 0.00000 ; alkenes all-atom CM C= C_2 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; acrolein CM C= C_2 O_2 3 30.33400 -5.23000 -25.10400 0.00000 0.00000 0.00000 ; acrolein CM CM C N 3 4.18400 -4.18400 0.00000 0.00000 0.00000 0.00000 ; vinyl amides CM CM C O 3 30.33400 -5.23000 -25.10400 0.00000 0.00000 0.00000 ; acrolein-like CM CM C OH 3 -5.85760 -6.69440 12.55200 0.00000 0.00000 0.00000 ; acrylic acid-like CM CM CT CT 3 0.52719 -6.39734 -1.69452 7.56467 0.00000 0.00000 ; alkenes CM CM CT HC 3 -0.77822 -2.33467 0.00000 3.11290 0.00000 0.00000 ; alkenes all-atom CM CM OS CT 3 5.23000 7.32200 -12.55200 0.00000 0.00000 0.00000 ; vinyl ether CM CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; CM CT CT HC 3 0.76567 2.29701 0.00000 -3.06269 0.00000 0.00000 ; alkene CM CT OH HO 3 -1.88280 1.88280 0.00000 0.00000 0.00000 0.00000 ; allyl alcohols CM OS CT HC 3 1.58992 4.76976 0.00000 -6.35968 0.00000 0.00000 ; ethers AA CN NA CW HA 3 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 ; chi-4 in TRP CO CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; hydrocarbon *new* 11/99 CO CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; acetal CO CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; amine all-atom CO CT OH HO 3 -0.44350 3.83255 0.72801 -4.11705 0.00000 0.00000 ; CO OS CT CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; CO OS CT HC 3 1.58992 4.76976 0.00000 -6.35968 0.00000 0.00000 ; ethers AA C_3 CT CT CT 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; carboxylate ion C_3 CT CT HC 3 -0.47070 -1.41210 0.00000 1.88280 0.00000 0.00000 ; carboxylate ion C_3 CT_2 CT CT 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; carboxylate ion C_3 CT_2 CT HC 3 -0.47070 -1.41210 0.00000 1.88280 0.00000 0.00000 ; carboxylate ion C_2 CT CT CT 3 -4.23421 7.22159 1.90790 -4.89528 0.00000 0.00000 ; aldehyde & ketone C_2 CT CT HC 3 -0.15899 -0.47698 0.00000 0.63596 0.00000 0.00000 ; aldehyde & ketone C_2 OS CT CT 3 -2.19660 5.20071 0.52719 -3.53130 0.00000 0.00000 ; esters C_2 OS CT HC 3 0.41421 1.24265 0.00000 -1.65686 0.00000 0.00000 ; esters CT_3 N C O 3 25.47638 0.00000 -25.47638 0.00000 0.00000 0.00000 ; CT_3 N C CT 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; CT_3 N C CT_2 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; CT_3 N CT_2 CT 3 6.87222 -9.94328 3.07105 0.00000 0.00000 0.00000 ; Pro CD-N-CA-CB CT_3 NT CT_2 CT 3 6.87222 -9.94328 3.07105 0.00000 0.00000 0.00000 ; Pro CD-N-CA-CB CT_3 N CT_2 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT_3 NT CT_2 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT_3 CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; CT_3 CT CT CT_2 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; CT_3 N3 CT_2 CT 3 6.87222 -9.94328 3.07105 0.00000 0.00000 0.00000 ; Pro CD-N-CA-CB CT_3 N3 CT_2 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CQ CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; aromatics CR CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; aromatics CR N* CT CT 3 -3.55640 2.09200 1.46440 0.00000 0.00000 0.00000 ; imidazoles, indoles, purines CR N* CT OS 3 -9.41400 3.13800 6.27600 0.00000 0.00000 0.00000 ; imidazoles, indoles, purines CR NA CT CT 3 -3.55640 2.09200 1.46440 0.00000 0.00000 0.00000 ; imidazoles, indoles, purines CR NA CT OS 3 -9.41400 3.13800 6.27600 0.00000 0.00000 0.00000 ; imidazoles, indoles, purines CR NA CW HA 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; CR NA CX CT 3 11.71520 0.00000 -11.71520 0.00000 0.00000 0.00000 ; chi-3 in HID, HIP CR NA CX CX 3 11.71520 0.00000 -11.71520 0.00000 0.00000 0.00000 ; chi-3 in HID, HIP CR NA CX HA 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; CS CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; CS CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; aromatics CT C C N 3 -0.20920 1.04600 -0.83680 0.00000 0.00000 0.00000 ; dicarbonyls CT C C O 3 2.09200 0.00000 -2.09200 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) CT C C CT 3 -4.81160 -1.46440 6.27600 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) CT C C HC 3 -1.50624 -1.67360 3.17984 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) CT C N H 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; amides C-C(O)-N-H CT C N CT 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; amides - V1 changed to 2.3 CT C N OH 3 39.31496 -2.94344 -27.62695 -8.74456 0.00000 0.00000 ; hydroxamic acids CT C CT CT 3 0.81797 -7.90567 0.60250 6.48520 0.00000 0.00000 ; ketone CT C CT HC 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone CT C NC CT 3 58.57600 0.00000 -58.57600 0.00000 0.00000 0.00000 ; imine CT C OH HO 3 26.15000 -3.13800 -23.01200 0.00000 0.00000 0.00000 ; carboxylic acid - aliphatic CT_2 C OH HO 3 26.15000 -3.13800 -23.01200 0.00000 0.00000 0.00000 ; COOH terminus CT C OS CT 3 31.20637 -9.76754 -21.43881 0.00000 0.00000 0.00000 ; esters CT N C O 3 25.47638 0.00000 -25.47638 0.00000 0.00000 0.00000 ; amides O-C(O)-N-C CT N C HC 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; amides - V1 changed to 2.3 CT N C OH 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; carbamates CT N C OS 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; carbamates CT N CA N2 3 33.20422 0.00000 -33.20422 0.00000 0.00000 0.00000 ; methylguanidinium ion CT N CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; tert. amide CT N SY CT 3 -2.89742 11.18174 12.40975 -20.69406 0.00000 0.00000 ; sulfonamide CT S S CT 3 -27.45332 10.70058 31.02018 -14.26744 0.00000 0.00000 ; disulfide all-atom CT S CT HC 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; sulfide all-atom CT C+ CT CT 3 -4.18400 0.00000 4.18400 0.00000 0.00000 0.00000 ; carbocation CT C+ CT HC 3 -4.18400 0.00000 4.18400 0.00000 0.00000 0.00000 ; carbocation CT C= C= HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom CT C= CM CT 3 58.57600 0.00000 -58.57600 0.00000 0.00000 0.00000 ; alkene CT C= CM HC 3 58.57600 0.00000 -58.57600 0.00000 0.00000 0.00000 ; alkene CT CM C= HC 3 58.57600 0.00000 -58.57600 0.00000 0.00000 0.00000 ; alkene CT CM CT CT 3 6.32202 -2.48530 0.70710 -4.54382 0.00000 0.00000 ; alkenes CT CM CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom CT CM OS CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; ethers AA CT CO OS CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; ethers AA CT CT C F 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; acyl halide CT CT C N 3 4.83252 -7.65254 1.68196 1.13805 0.00000 0.00000 ; propanamide CT CT C O 3 4.87855 0.00000 -4.87855 0.00000 0.00000 0.00000 ; propanamide CT_2 CT C O 3 4.87855 0.00000 -4.87855 0.00000 0.00000 0.00000 ; Sidechain. CT CT C Cl 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; acyl halide CT CT C HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aldehyde CT CT C OH 3 5.31786 0.73220 -2.28446 -3.76560 0.00000 0.00000 ; RCOOH acid CT_2 CT C OH 3 5.31786 0.73220 -2.28446 -3.76560 0.00000 0.00000 ; RCOOH acid CT CT_2 C OH 3 5.31786 0.73220 -2.28446 -3.76560 0.00000 0.00000 ; COOH terminus CT CT C OS 3 -1.15688 -3.47063 0.00000 4.62750 0.00000 0.00000 ; esters CT CT C O_3 3 2.28446 0.00000 -2.28446 0.00000 0.00000 0.00000 ; RCOOH acid CT_2 CT C O_3 3 2.28446 0.00000 -2.28446 0.00000 0.00000 0.00000 ; RCOOH acid CT CT_2 C O_3 3 2.28446 0.00000 -2.28446 0.00000 0.00000 0.00000 ; COOH terminus CT_2 CT C_3 O2 3 2.28446 0.00000 -2.28446 0.00000 0.00000 0.00000 ; COOH terminus CT CT N H 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; N-ethylformamide, peptides CT CT N CY 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; small ring amides CT CT N SY 3 -3.43088 -3.00830 10.59807 -4.15890 0.00000 0.00000 ; sulfonamide CT CT S S 3 2.51876 1.80749 3.49782 -7.82408 0.00000 0.00000 ; disulfide all-atom CT CT S CT 3 0.94140 2.31375 2.40999 -5.66514 0.00000 0.00000 ; sulfide all-atom CT CT C* CW 3 -1.49369 1.49369 0.00000 0.00000 0.00000 0.00000 ; 3-ethylindole CT_2 CT C* CW 3 -1.49369 1.49369 0.00000 0.00000 0.00000 0.00000 ; TRP Chi-2 CT CT C+ HC 3 -4.18400 0.00000 4.18400 0.00000 0.00000 0.00000 ; carbocation CT CT CO HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; acetal CT CT CS CW 3 -1.49369 1.49369 0.00000 0.00000 0.00000 0.00000 ; 3-ethylindole CT CT CT F 3 1.46440 1.88280 0.00000 -3.34720 0.00000 0.00000 ; alkyl fluoride CT CT CT N 3 5.48732 0.02719 0.00000 -5.51451 0.00000 0.00000 ; N-propylformamide CT CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; sulfide all-atom CT CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; hydrocarbon all-atom CT CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; butanamide CT CT CT Cl 3 0.83680 2.51040 0.00000 -3.34720 0.00000 0.00000 ; alkyl chloride CT CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom CT CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; CT CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; ammonium ion all-atom CT CT CT NA 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; CT CT CT NC 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; CT CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; amine all-atom CT CT CT_2 NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; H2N-terminus. CT CT CT NY 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; CT CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; alcohols, ethers AA CT CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; alcohols, ethers AA CT CT CT SH 3 2.78446 0.27823 0.82844 -3.89112 0.00000 0.00000 ; thiol all-atom CT CT CT SY 3 2.78446 0.27823 0.82844 -3.89112 0.00000 0.00000 ; thiol all-atom (mod 11/99) CT CT CT CT_2 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; peptide sidechain CT CT CT SY2 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; CT CT CV CW 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT CT CV NB 3 4.90992 -1.78029 1.09621 -4.22584 0.00000 0.00000 ; 5-ethylimidazole CT CT CW NA 3 1.04600 -3.55640 2.51040 0.00000 0.00000 0.00000 ; 2-ethyl pyrrole CT CT CZ CZ 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; alkynes CT CT N2 H 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; guanidinium CT CT N2 H3 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; amine all-atom, CT CT N3 H 3 0.72592 2.17777 0.00000 -2.90370 0.00000 0.00000 ; ammonium ion all-atom CT CT N3 CT 3 3.04176 -1.35144 0.51881 -2.20915 0.00000 0.00000 ; 2ary ammonium CT CT N3 H3 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; amine all-atom CT CT NC NZ 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; azides CT CT NO ON 3 1.67360 0.00000 -1.67360 0.00000 0.00000 0.00000 ; CT-CT-NO-ON nitroethane CT CT NT H 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; amine all-atom CT CT_3 NT H 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; amine all-atom CT CT_2 NT H 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; H2N-terminus CT CT NT CT 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; amine all-atom CT CT NY H 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; neutral ARG CT CT NY H3 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; neutral ARG CT CT OH HO 3 -0.44350 3.83255 0.72801 -4.11705 0.00000 0.00000 ; alcohols AA CT CT_4 OH HO 3 0.26778 -9.36798 9.10020 0.00000 0.00000 0.00000 ; trifluoroethanol CT CT OS CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; ethers AA CT CT P+ CT 3 1.04600 1.04600 2.09200 -4.18400 0.00000 0.00000 ; phosphonium ion CT CT SH HS 3 -1.34516 5.85551 1.17989 -5.69024 0.00000 0.00000 ; thiol all-atom (mod 11/99) CT CT SY N 3 0.00628 -4.19864 3.21331 0.97905 0.00000 0.00000 ; sulfonamide CT CT C_3 O2 3 3.43088 0.00000 -3.43088 0.00000 0.00000 0.00000 ; carboxylate ion CT CT_2 C_3 O2 3 3.43088 0.00000 -3.43088 0.00000 0.00000 0.00000 ; carboxylate ion CT CT C_2 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aldehyde CT CT C_2 OS 3 -1.15688 -3.47063 0.00000 4.62750 0.00000 0.00000 ; esters CT CT C_2 O_2 3 3.10662 -3.77606 -5.13795 5.80739 0.00000 0.00000 ; aldehyde & ketone CT CT CT_3 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; CT CT CT_3 NT 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; CT CT CT_3 HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; CT CT CT_3 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CT CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CT CT CT_2 HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom CT CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CT CT SY2 CT 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfone CT CT SY2 OY 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfone CT CX NA H 3 11.71520 0.00000 -11.71520 0.00000 0.00000 0.00000 ; chi-3 in HID, HIP CT CY CY CY 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; cycropropane CT CY CY HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; small ring *new* 11/99 CT N2 CA N 3 33.20422 0.00000 -33.20422 0.00000 0.00000 0.00000 ; methylguanidinium ion CT N2 CA N2 3 33.20422 0.00000 -33.20422 0.00000 0.00000 0.00000 ; methylguanidinium ion CT NY CA NZ 3 33.20422 0.00000 -33.20422 0.00000 0.00000 0.00000 ; ARGN. CT NY CA NY 3 33.20422 0.00000 -33.20422 0.00000 0.00000 0.00000 ; ARGN. CT N3 CT HC 3 0.63179 1.89535 0.00000 -2.52714 0.00000 0.00000 ; 2ary ammonium CT NC NZ NZ 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; azides CT NT CT HC 3 1.17152 3.51456 0.00000 -4.68608 0.00000 0.00000 ; amine all-atom CT NT NT H 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; generic CT NT NT CT 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; generic hydrazines CT NT OH HO 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; generic CT NT OS CT 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; generic hydroxylamines CT OS C N 3 16.73600 4.18400 -20.92000 0.00000 0.00000 0.00000 ; carbamates CT OS C O 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ; benzoic acids & esters CT OS C HC 3 31.20637 -9.76754 -21.43881 0.00000 0.00000 0.00000 ; esters CT OS P CT 3 -3.34720 2.09200 13.80720 -12.55200 0.00000 0.00000 ; phosphonates CT OS P O2 3 1.17570 3.52711 0.00000 -4.70281 0.00000 0.00000 ; Me2PO4 (-) CT OS P OS 3 1.04600 3.13800 10.04160 -4.18400 0.00000 0.00000 ; Me2PO4 (-), from Amber. CT OS CM HC 3 1.58992 4.76976 0.00000 -6.35968 0.00000 0.00000 ; ethers AA CT OS CO HC 3 1.58992 4.76976 0.00000 -6.35968 0.00000 0.00000 ; ethers AA CT OS CO OH 3 -6.45801 0.80961 5.68187 -0.03347 0.00000 0.00000 ; hexopyranoses CT OS CO OS 3 -6.45801 0.80961 5.68187 -0.03347 0.00000 0.00000 ; hexopyranoses CT OS CT HC 3 1.58992 4.76976 0.00000 -6.35968 0.00000 0.00000 ; ethers AA CT OS CT OH 3 -5.35761 13.61683 8.44331 -16.70253 0.00000 0.00000 ; acetals AA CT OS CT OS 3 -5.35761 13.61683 8.44331 -16.70253 0.00000 0.00000 ; acetals AA CT OS NT H 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; generic CT OS C_2 HC 3 31.20637 -9.76754 -21.43881 0.00000 0.00000 0.00000 ; esters CT OS C_2 O_2 3 21.43881 0.00000 -21.43881 0.00000 0.00000 0.00000 ; esters CT P+ CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; phosphonium ion CT SY N H 3 -15.61050 0.70291 20.50579 -5.59819 0.00000 0.00000 ; sulfonamide CT C_2 C= HC 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone CT C_2 CT CT 3 0.81797 -7.90567 0.60250 6.48520 0.00000 0.00000 ; ketone CT C_2 CT HC 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone CT C_2 OS CT 3 31.20637 -9.76754 -21.43881 0.00000 0.00000 0.00000 ; esters CT CT_3 N CT_2 3 -8.97677 -76.68644 -8.61067 94.27389 0.00000 0.00000 ; Pro CG-CD-N-CA CT CT_3 NT CT_2 3 -8.97677 -76.68644 -8.61067 94.27389 0.00000 0.00000 ; Pro CG-CD-N-CA CT CT_3 N3 H3 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; amine all-atom, CT CT_3 N3 CT_2 3 -8.97677 -76.68644 -8.61067 94.27389 0.00000 0.00000 ; Pro CG-CD-N-CA CT CT_2 C N 3 5.00825 -1.69870 -0.37238 -2.93716 0.00000 0.00000 ; Psi prime peptides AA CT CT_2 C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides X-CT_2-C(O)-O CT CT_2 N H 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides H-N-CA-R CT CT_2 N3 H3 3 0.72592 2.17777 0.00000 -2.90370 0.00000 0.00000 ; peptides H-N-CA-R CT SY2 CT HC 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; sulfone CT_2 C N H 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; peptide C-C(O)-N-H CT_2 C N CT_2 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; peptide - V1 changed to 2.3 CT C N CT_2 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; peptide for ACE CT N C CT_2 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; peptide for NAC CT_2 N C O 3 25.47638 0.00000 -25.47638 0.00000 0.00000 0.00000 ; peptide O-C(O)-N-C CT_2 N C HC 3 30.28798 -4.81160 -25.47638 0.00000 0.00000 0.00000 ; peptide - V1 changed to 2.3 CT_2 N CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptide tert. amide CT_2 N CT_3 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT_2 NT CT_3 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT_2 N CT_2 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptide tert. amide CT CT C O2 3 2.28446 0.00000 -2.28446 0.00000 0.00000 0.00000 ; ASP CT_2 CT C O2 3 2.28446 0.00000 -2.28446 0.00000 0.00000 0.00000 ; ASP CT_2 CT C N 3 -9.49768 -6.36386 8.89936 6.96218 0.00000 0.00000 ; ASN CT_2 CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; MET CT_2 CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom CT_2 CT CV CW 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT_2 CT CV NB 3 4.73838 -1.52507 1.30541 -4.51872 0.00000 0.00000 ; HID, HIE, HIP CT_2 CT CW CV 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT_2 CT CW NA 3 4.73838 -1.52507 1.30541 -4.51872 0.00000 0.00000 ; HID, HIE, HIP CT_2 CT CX CX 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CT_2 CT CX NA 3 4.73838 -1.52507 1.30541 -4.51872 0.00000 0.00000 ; HID, HIE, HIP CT_2 CT OH HO 3 -4.16308 6.71114 3.63590 -6.18395 0.00000 0.00000 ; Ser & Thr 02/00 CT_2 CT SH HS 3 -1.50624 5.37225 1.17989 -5.04590 0.00000 0.00000 ; thiol all-atom CT_2 N3 CT_3 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CU CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; aromatics CU CT SY N 3 0.00628 -4.19864 3.21331 0.97905 0.00000 0.00000 ; sulfonamide CV CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; aromatics CV CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CV CT CT_2 HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; CV CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CV CW CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; HID, HIE, HIP, Also Use: H-C-C-C(bz) CW C* CT HC 3 -1.00416 -3.01248 0.00000 4.01664 0.00000 0.00000 ; 3-methylindole CW CS CT HC 3 -1.00416 -3.01248 0.00000 4.01664 0.00000 0.00000 ; 3-methylindole CW CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; aromatics CW CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CW CT CT_2 HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; CW CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CW CV CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; HID, HIE, HIP, Also Use: H-C-C-C(bz) CW NA CR HA 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; chi-4 in HID, &chi-4,4 prime,5 in HIP CW NA CR NB 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; chi-4 in HID, chi-5 in HIE CX CT CT HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; CX CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides CX CT CT_2 HC 3 0.96650 2.89951 0.00000 -3.86601 0.00000 0.00000 ; CX CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; Chi-1 peptides AA CX CX CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; HID, HIE, HIP, Also Use: H-C-C-C(bz) CX CX NA H 3 11.71520 0.00000 -11.71520 0.00000 0.00000 0.00000 ; chi-3 in HID, HIP CX N2 CA N2 3 33.20422 0.00000 -33.20422 0.00000 0.00000 0.00000 ; methylguanidinium ion CX NA CR HA 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; chi-5 in HIE CX NA CR NA 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; chi-5 in HIE CY N C O 3 25.47638 0.00000 -25.47638 0.00000 0.00000 0.00000 ; small ring amides CY CY N H 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; small ring CY CY CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; small ring *new* 11/99 CY CY CY HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom CZ CT CT HC 3 0.76567 2.29701 0.00000 -3.06269 0.00000 0.00000 ; alkyne, nitrile CZ CZ CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; alkynes Cl C CT HC 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ; acyl halide Cl CM CM Cl 3 55.22880 3.34720 -58.57600 0.00000 0.00000 0.00000 ; chloroalkene Cl CT CT Cl 3 -0.52300 0.52300 0.00000 0.00000 0.00000 0.00000 ; dichloride Cl CT CT HC 3 0.83680 2.51040 0.00000 -3.34720 0.00000 0.00000 ; alkyl chloride Cl CT CT NT 3 4.18400 -4.18400 0.00000 0.00000 0.00000 0.00000 ; 2-chloroethylamin F C CT HC 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ; acyl halide F CT CT F 3 -5.23000 5.23000 0.00000 0.00000 0.00000 0.00000 ; 1,2-difluoride F CT CT HC 3 0.83680 2.51040 0.00000 -3.34720 0.00000 0.00000 ; alkyl fluoride F CT CT OH 3 1.12968 3.38904 0.00000 -4.51872 0.00000 0.00000 ; trifluoroethanol F CT CT_4 HC 3 0.65689 1.97066 0.00000 -2.62755 0.00000 0.00000 ; trifluoroethanol F CT CT_4 OH 3 1.12968 3.38904 0.00000 -4.51872 0.00000 0.00000 ; trifluoroethanol H N C N 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; imides H N C O 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; amides wlj 6/20/97 H N C HC 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; amides H N C OH 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; carbamates H N C OS 3 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; carbamates H N CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; N-methylformamide H N CY HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; small ring H N OH HO 3 -15.86991 -5.69442 21.56434 0.00000 0.00000 0.00000 ; hydroxamic acids H N CT_2 HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides H-N-CA-HC H N CT_2 C 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides H-N-CA-CT H N2 CA N2 3 16.31760 0.00000 -16.31760 0.00000 0.00000 0.00000 ; guanidinium ion H N2 CA NC 3 2.92880 -2.92880 0.00000 0.00000 0.00000 0.00000 ; Adenine RZ H N2 CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; methylguanidinium ion H N3 CT HC 3 0.54601 1.63803 0.00000 -2.18405 0.00000 0.00000 ; ammonium ion all-atom H NA CR HA 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; chi-4 in HID H NA CR NA 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; chi-5 in HIE H NA CR NB 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; chi-4 in HID H NA CW HA 3 12.55200 0.00000 -12.55200 0.00000 0.00000 0.00000 ; chi-4 in TRP H NA CX HA 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; chi-4 prime in HIE H NT CT HC 3 0.83680 2.51040 0.00000 -3.34720 0.00000 0.00000 ; amine all-atom H NT CT_3 HC 3 0.83680 2.51040 0.00000 -3.34720 0.00000 0.00000 ; amine all-atom H NT CT_2 HC 3 0.83680 2.51040 0.00000 -3.34720 0.00000 0.00000 ; H2N-terminus H NT NT H 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; generic H NT OH HO 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; generic H NY CA NY 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; neutral ARG H3 NY CA NY 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; neutral ARG H NY CA NZ 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; neutral ARG H3 NY CA NZ 3 -1.26775 3.02085 1.74473 -3.49782 0.00000 0.00000 ; neutral ARG H3 N2 CA N2 3 16.31760 0.00000 -16.31760 0.00000 0.00000 0.00000 ; guanidinium ion H3 N2 CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; methylguanidinium ion H3 N3 CT_3 HC 3 0.54601 1.63803 0.00000 -2.18405 0.00000 0.00000 ; peptides H-N-CA-HC H3 N3 CT_2 HC 3 0.54601 1.63803 0.00000 -2.18405 0.00000 0.00000 ; peptides H-N-CA-HC H3 N3 CT HC 3 0.54601 1.63803 0.00000 -2.18405 0.00000 0.00000 ; ammonium ion all-atom H3 NY CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; methylguanidinium ion H3 NZ CA NY 3 16.31760 0.00000 -16.31760 0.00000 0.00000 0.00000 ; ARGN HC C C N 3 -0.62760 1.88280 -1.25520 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) HC C C O 3 0.83680 0.00000 -0.83680 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) HC C C HC 3 1.67360 -1.67360 0.00000 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) HC C CT HC 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ; aldehyde HC C NC HC 3 58.57600 0.00000 -58.57600 0.00000 0.00000 0.00000 ; imine HC C OH HO 3 26.15000 -3.13800 -23.01200 0.00000 0.00000 0.00000 ; carboxylic acid - aliphatic HC C= C= HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HC C= CM HC 3 58.57600 0.00000 -58.57600 0.00000 0.00000 0.00000 ; alkene HC C= C_2 O_2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; acrolein HC CM C N 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; HC CM C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; HC CM CT HC 3 0.66525 1.99576 0.00000 -2.66102 0.00000 0.00000 ; alkene HC CT C N 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; acetamide HC CT C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; all carbonyls HC CT C O2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; caboxylates HC CT C OH 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; RCOOH acid HC CT C OS 3 0.27615 0.82844 0.00000 -1.10458 0.00000 0.00000 ; esters HC CT C O_2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aldehyde, ketone, ester HC CT C O_3 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; RCOOH acid HC CT N SY 3 -2.93508 -1.91418 6.09609 -1.24684 0.00000 0.00000 ; sulfonamide HC CT P O2 3 0.52300 1.56900 0.00000 -2.09200 0.00000 0.00000 ; phosphonates HC CT P OS 3 0.52300 1.56900 0.00000 -2.09200 0.00000 0.00000 ; phosphonates HC CT S S 3 1.16734 3.50201 0.00000 -4.66935 0.00000 0.00000 ; disulfide all-atom HC CT CA N2 3 -4.09614 5.08775 2.96645 -3.95806 0.00000 0.00000 ; MDDR amine all-atom HC CT CA NT 3 -4.09614 5.08775 2.96645 -3.95806 0.00000 0.00000 ; amine all-atom HC CT CO OS 3 0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000 ; alcohols, ethers AA HC CT CT N 3 0.97069 2.91206 0.00000 -3.88275 0.00000 0.00000 ; N-ethylformamide HC CT CT S 3 0.94559 2.83675 0.00000 -3.78234 0.00000 0.00000 ; sulfide all-atom HC CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon *new* 11/99 HC CT CT N2 3 -1.21755 -3.65264 0.00000 4.87018 0.00000 0.00000 ; ethylguanidinium ion HC CT CT N3 3 0.80333 2.40999 0.00000 -3.21331 0.00000 0.00000 ; ammonium ion all-atom HC CT CT NO 3 -0.47070 -1.41210 0.00000 1.88280 0.00000 0.00000 ; nitroethane HC CT CT NT 3 -4.09614 5.08775 2.96645 -3.95806 0.00000 0.00000 ; amine all-atom HC CT CT_2 NT 3 -4.09614 5.08775 2.96645 -3.95806 0.00000 0.00000 ; H2N-terminus HC CT CT NY 3 -1.21755 -3.65264 0.00000 4.87018 0.00000 0.00000 ; ARGN. HC CT CT OH 3 0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000 ; alcohols, ethers AA HC CT CT OS 3 0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000 ; alcohols, ethers AA HC CT CT P+ 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; phosphonium ion HC CT CT SH 3 0.94559 2.83675 0.00000 -3.78234 0.00000 0.00000 ; thiol all-atom HC CT CT SY2 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; sulfone HC CT CT SY 3 0.94559 2.83675 0.00000 -3.78234 0.00000 0.00000 ; sulfide all-atom HC CT CU NB 3 0.87864 2.63592 0.00000 -3.51456 0.00000 0.00000 ; from HC-CT-CV-NB HC CT CV NB 3 0.87864 2.63592 0.00000 -3.51456 0.00000 0.00000 ; HID, HIE, HIP HC CT CW NA 3 0.87864 2.63592 0.00000 -3.51456 0.00000 0.00000 ; HID, HIE, HIP Also Use: H-C-C-N HC CT CX NA 3 0.87864 2.63592 0.00000 -3.51456 0.00000 0.00000 ; HID, HIE, HIP HC CT NO ON 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; HC-CT-NO-ON nitro compounds HC CT OH HO 3 0.94140 2.82420 0.00000 -3.76560 0.00000 0.00000 ; alcohols AA HC CT_4 OH HO 3 0.99579 2.98738 0.00000 -3.98316 0.00000 0.00000 ; trifluoroethanol HC CT OS P 3 0.74684 2.24053 0.00000 -2.98738 0.00000 0.00000 ; Me2PO4 (-) HC CT SH HS 3 1.00416 3.01248 0.00000 -4.01664 0.00000 0.00000 ; thiol all-atom (mod 11/99) HC CT SY N 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide HC CT C_3 O2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; carboxylate ion HC CT_2 C_3 O2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; carboxylate ion HC CT C_2 OS 3 0.27615 0.82844 0.00000 -1.10458 0.00000 0.00000 ; esters HC CT C_2 O_2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aldehyde, ketone, ester HC CT CT_3 N 3 0.97069 2.91206 0.00000 -3.88275 0.00000 0.00000 ; HC CT CT_3 NT 3 0.97069 2.91206 0.00000 -3.88275 0.00000 0.00000 ; HC CT CT_3 N3 3 0.97069 2.91206 0.00000 -3.88275 0.00000 0.00000 ; N-ethylformamide HC CT CT_2 N 3 0.97069 2.91206 0.00000 -3.88275 0.00000 0.00000 ; peptide HC CT CT_2 HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom HC CT CT_2 N3 3 0.97069 2.91206 0.00000 -3.88275 0.00000 0.00000 ; peptide HC CT SY2 OY 3 0.73220 2.19660 0.00000 -2.92880 0.00000 0.00000 ; sulfone HC CY CY HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; small ring *new* 11/99 HC NC NZ NZ 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; azides HC C_2 CT HC 3 0.75312 2.25936 0.00000 -3.01248 0.00000 0.00000 ; aldehyde HC CT_3 CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HC CT_2 C N 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; Psi bis peptides AA HC CT_2 C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides HC-CA-C(O)-O HC CT_2 C OH 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; RCOOH acid HC CT_2 C O_3 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; RCOOH acid HC CT_2 CT S 3 0.94559 2.83675 0.00000 -3.78234 0.00000 0.00000 ; thiol all-atom HC CT_2 CT OH 3 0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000 ; alcohols, ethers AA HC CT_2 CT SH 3 0.94559 2.83675 0.00000 -3.78234 0.00000 0.00000 ; thiol all-atom HO OH C N 3 16.73600 4.18400 -20.92000 0.00000 0.00000 0.00000 ; carbamates HO OH C O 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ; benzoic acids & ester HO OH C O_3 3 23.01200 0.00000 -23.01200 0.00000 0.00000 0.00000 ; carboxylic acid - aliphatic HO OH P O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; phosphonates HO OH P OH 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; phosphonates HO OH CO OS 3 -10.17967 2.64847 7.55630 -0.02510 0.00000 0.00000 ; hexopyranoses N C C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) N C CT_2 N 3 10.36376 -6.60654 -10.49347 6.73624 0.00000 0.00000 ; Psi peptides AA N-CA-C(O)-N N C CT_2 N3 3 10.36376 -6.60654 -10.49347 6.73624 0.00000 0.00000 ; Psi peptides AA N-CA-C(O)-N N C CT_2 NT 3 10.36376 -6.60654 -10.49347 6.73624 0.00000 0.00000 ; Psi peptides AA N-CA-C(O)-N N CA CT NT 3 19.59994 -21.39070 4.05011 -2.25936 0.00000 0.00000 ; MDDR amine all-atom N CT C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides N CT_2 C O_3 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; COOH terminus N CT_2 C OH 3 14.43480 -11.00392 -3.43088 0.00000 0.00000 0.00000 ; COOH terminus, guess from NT NT CT_2 C O_3 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; COOH terminus NT CT_2 C OH 3 14.43480 -11.00392 -3.43088 0.00000 0.00000 0.00000 ; COOH terminus, guess from NT N CT C_3 O2 3 3.43088 0.00000 -3.43088 0.00000 0.00000 0.00000 ; carboxylate ion N CT_2 C_3 O2 3 3.43088 0.00000 -3.43088 0.00000 0.00000 0.00000 ; carboxylate ion N CT_2 C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides N-CA-C(O)-O N CT_2 CT S 3 3.40787 -2.80537 -0.35982 -0.24267 0.00000 0.00000 ; Chi for Cyx, N CT_2 CT OH 3 9.89307 -4.71746 3.67774 -8.85335 0.00000 0.00000 ; Chi for Ser & Thr N CT_2 CT SH 3 3.40787 -2.80537 -0.35982 -0.24267 0.00000 0.00000 ; Chi for Cys N3 CT_2 C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides X-CT_2-C(O)-O N3 CT_2 C_3 O2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; Zwitterion AAs N3 CT_2 CT S 3 3.40787 -2.80537 -0.35982 -0.24267 0.00000 0.00000 ; Chi for Cyx, N3 CT_2 CT OH 3 9.89307 -4.71746 3.67774 -8.85335 0.00000 0.00000 ; Chi for Ser & Thr N3 CT_2 CT SH 3 3.40787 -2.80537 -0.35982 -0.24267 0.00000 0.00000 ; Chi for Cys N3 CT CT OH 3 9.89307 -4.71746 3.67774 -8.85335 0.00000 0.00000 ; NT CA CT NT 3 19.59994 -21.39070 4.05011 -2.25936 0.00000 0.00000 ; amine all-atom NT CT C OH 3 14.43480 -11.00392 -3.43088 0.00000 0.00000 0.00000 ; RCOOH acid NT CT CT NT 3 19.59994 -21.39070 4.05011 -2.25936 0.00000 0.00000 ; amine all-atom NT CT CT OH 3 16.73600 -16.73600 0.00000 0.00000 0.00000 0.00000 ; 2-aminoethanol 6-31G* fit - wj NT CT_2 CT OH 3 16.73600 -16.73600 0.00000 0.00000 0.00000 0.00000 ; H2N-terminus NT CT_2 C O 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; H2N-terminus NT CT_2 CT S 3 3.40787 -2.80537 -0.35982 -0.24267 0.00000 0.00000 ; H2N-terminus NT CT_2 CT SH 3 3.40787 -2.80537 -0.35982 -0.24267 0.00000 0.00000 ; H2N-terminus O C C O 3 16.73600 -3.34720 -13.38880 0.00000 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) O C N OH 3 27.62695 0.00000 -27.62695 0.00000 0.00000 0.00000 ; hydroxamic acids OH CT CT OH 3 18.96607 -18.96607 0.00000 0.00000 0.00000 0.00000 ; hexopyranoses OH CT CT OS 3 9.03534 -9.03534 0.00000 0.00000 0.00000 0.00000 ; hexopyranoses OS CT CT OS 3 -1.15060 1.15060 0.00000 0.00000 0.00000 0.00000 ; polyethers, crown ethers CA CA N X 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; N-phenylamide CT CT CK X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CA CA CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; ethyl benzene NZ CZ CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; nitriles O C CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides CT CT C* X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CQ X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CR X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CS X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CU X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CV X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics OY SY N X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY C3 X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY CA X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY OY X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY NT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide CT CT CW X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CZ CZ CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; alkynes Cl CT CS X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; chloromethyl aromatic Cl CT CW X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; chloromethyl aromatic F CT CS X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; fluoromethyl aromatic H N CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides F CT CW X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; fluoromethyl aromatic H N CT_2 X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides H-N-CA-X H N2 CA X 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline-like H3 NY CA X 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline-like (used for ARGN) H N2 CQ X 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline-like H NA CB X 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; H NA CR X 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; H NA CW X 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; HA CR NA X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; HC CT C* X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CK X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CQ X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CR X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CS X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CU X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CV X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CW X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics N SY CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide X C CB X 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; X C CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X C* CB X 3 14.01640 0.00000 -14.01640 0.00000 0.00000 0.00000 ; X C* CW X 3 54.60120 0.00000 -54.60120 0.00000 0.00000 0.00000 ; X CA S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with S X CA CA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA CB X 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; X CA CN X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CA CR X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA CU X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA CW X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with O X CB N X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CB CB X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CB CN X 3 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; X CB CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CB NA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CB NB X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CB NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CK NA X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CK NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CK NC X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CM CM X 3 58.57600 0.00000 -58.57600 0.00000 0.00000 0.00000 ; alkene X CN NA X 3 12.76120 0.00000 -12.76120 0.00000 0.00000 0.00000 ; X CQ N X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CQ NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CR S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring thiazole X CR CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CR NA X 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; X CR NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CR NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CR OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring oxazole X CS CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CS CW X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CU NB X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CV CW X 3 44.97800 0.00000 -44.97800 0.00000 0.00000 0.00000 ; X CV NA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CV NB X 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; X CW S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring thiazole X CW CW X 3 44.97800 0.00000 -44.97800 0.00000 0.00000 0.00000 ; X CW NA X 3 11.71520 0.00000 -11.71520 0.00000 0.00000 0.00000 ; X CW NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CW OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring furan X CY S X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; small ring X CY CY X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; small ring X CZ CZ X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; alkynes X NA S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with S X NA NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X NA OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with O X NB OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring isoxazole X NC NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X OS S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with S X CX CX X 3 44.97800 0.00000 -44.97800 0.00000 0.00000 0.00000 ; CT CT CO OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CT CT CO OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA HC CM CT OH 3 0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA HC CM CT OS 3 0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CT CM CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CT CM CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CA CA CT OH 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) benzyl alcohols & ethers CA CA CT OS 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) benzyl alcohols & ethers CT CT NA CB 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CT CT NA CW 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CA CT NA CB 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CA CT NA CK 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CA CT NA CR 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CA CT NA CW 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CB NA CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CK NA CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CR NA CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CW NA CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CT CT N* CM 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CT CT N* C 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CT CT N* C_2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CT CT N* C_3 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CT CT N* CB 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CM N* CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles C N* CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles C_2 N* CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles C_3 N* CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CB N* CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CK N* CT HC 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) heterocycles CA CA CT NT 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) aromatics CA CA CT N 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) aromatics CA CA CT NA 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) aromatics CA OS P O2 3 1.17570 3.52711 0.00000 -4.70281 0.00000 0.00000 ; (From wildcard) MeOPO3 (2-) mll C3 OS P O2 3 1.17570 3.52711 0.00000 -4.70281 0.00000 0.00000 ; (From wildcard) MeOPO3 (2-) mll CT OS CT N 3 -5.23000 7.32200 6.27600 -8.36800 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines CT OS CT N* 3 -5.23000 7.32200 6.27600 -8.36800 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines H N2 CA N 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; (From wildcard) aniline-like H N2 CA NA 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; (From wildcard) aniline-like C CT CT Cl 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CM 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CO 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT C 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT C_2 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CT_3 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CZ 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT C_3 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CB 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CR 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CV 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CW 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CX 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CS 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT C+ 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C= CM CT OH 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) allyl alcohols, ethers C= CM CT OS 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) allyl alcohols, ethers CA CT S S 3 2.51876 1.80749 3.49782 -7.82408 0.00000 0.00000 ; (From wildcard) disulfide all-atom CT_2 CT S S 3 2.51876 1.80749 3.49782 -7.82408 0.00000 0.00000 ; (From wildcard) disulfide all-atom CW CT S S 3 2.51876 1.80749 3.49782 -7.82408 0.00000 0.00000 ; (From wildcard) disulfide all-atom Cl CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CM CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CO CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom C CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom C_2 CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CT_3 CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CZ CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom C_3 CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CB CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom C* CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CR CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CV CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CW CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CX CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom CS CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom C+ CT CT S 3 3.42461 -3.85974 2.59408 -2.15895 0.00000 0.00000 ; (From wildcard) sulfide all-atom Cl CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CM CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CA CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CO CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CT_2 CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C_2 CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CT_3 CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CZ CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C_3 CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CB CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C* CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CR CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CV CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CW CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CX CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide CS CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide C+ CT CT CU 3 -4.96013 6.28646 1.30959 -2.63592 0.00000 0.00000 ; (From wildcard) butanamide Cl CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CM CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CA CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CO CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CT_2 CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) C CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) C_2 CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CT_3 CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CZ CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) C_3 CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CB CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) C* CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CR CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CV CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CW CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CX CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CS CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) C+ CT CT N2 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) CM CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom CT_2 CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom C CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom C CT CT_2 NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; H2N-terminus C_2 CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom CT_3 CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom CZ CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom C_3 CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom C_3 CT CT_2 NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; H2N-terminus CB CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom C* CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom C* CT CT_2 NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; H2N-terminus CR CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom CV CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom CW CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom CX CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom CV CT CT_2 NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; H2N-terminus CW CT CT_2 NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; H2N-terminus CX CT CT_2 NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; H2N-terminus CS CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom C+ CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.00000 0.00000 ; (From wildcard) amine all-atom Cl CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CM CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CO CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CT_2 CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C_2 CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CT_3 CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CZ CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C_3 CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CB CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C* CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CR CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CV CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CW CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CX CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CS CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C+ CT CT OH 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA Cl CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CM CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CO CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CT_2 CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C_2 CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CT_3 CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CZ CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C_3 CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CB CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C* CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CR CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CV CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CW CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CX CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA CS CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA C+ CT CT OS 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 ; (From wildcard) alcohols, ethers AA Cl CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CM CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CA CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CO CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CT_2 CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom C CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom C_2 CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CT_3 CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CZ CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom C_3 CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CB CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom C* CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CR CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CV CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CW CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CX CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom CS CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom C+ CT CT SH 3 3.92459 -3.92459 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) thiol all-atom Cl CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CM CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CA CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CO CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CT_2 CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion C_2 CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CT_3 CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CZ CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion C_3 CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CB CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion C* CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CR CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CV CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CW CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CX CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CS CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion C+ CT CT C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CA CT CT_2 C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion C CT CT_2 C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion C_2 CT CT_2 C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion C_3 CT CT_2 C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion C* CT CT_2 C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CV CT CT_2 C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CW CT CT_2 C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion CX CT CT_2 C_3 3 -9.08346 9.75709 3.45180 -4.12542 0.00000 0.00000 ; (From wildcard) carboxylate ion Cl CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CM CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CO CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CT_2 CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom C CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom C_2 CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CT_3 CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CZ CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom C_3 CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CB CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom C* CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CR CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CV CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CW CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CX CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom CS CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom C+ CT CT N3 3 5.77183 -2.67148 0.95814 -4.05848 0.00000 0.00000 ; (From wildcard) ammonium ion all-atom C CT NT CT 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_2 CT NT CT 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_3 CT NT CT 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C3 CT NT CT 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CM CT OS CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; (From wildcard) ethers AA C CT OS CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; (From wildcard) ethers AA C_2 CT OS CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; (From wildcard) ethers AA C_3 CT OS CT 3 1.71544 2.84512 1.04600 -5.60656 0.00000 0.00000 ; (From wildcard) ethers AA C CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; (From wildcard) Chi-1 peptides AA C_2 CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; (From wildcard) Chi-1 peptides AA C_3 CT CT_2 N 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; (From wildcard) Chi-1 peptides AA C CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; (From wildcard) Chi-1 peptides AA C_2 CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; (From wildcard) Chi-1 peptides AA C_3 CT CT_2 N3 3 -0.76567 2.70705 4.02501 -5.96639 0.00000 0.00000 ; (From wildcard) Chi-1 peptides AA CM N* CT OS 3 -3.13800 -3.13800 6.27600 0.00000 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines C N* CT OS 3 -3.13800 -3.13800 6.27600 0.00000 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines C_2 N* CT OS 3 -3.13800 -3.13800 6.27600 0.00000 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines C_3 N* CT OS 3 -3.13800 -3.13800 6.27600 0.00000 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines CB N* CT OS 3 -3.13800 -3.13800 6.27600 0.00000 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines CB NA CT OS 3 -3.13800 -3.13800 6.27600 0.00000 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines CW NA CT OS 3 -3.13800 -3.13800 6.27600 0.00000 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines Cl CT_2 C N 3 5.00825 -1.69870 -0.37238 -2.93716 0.00000 0.00000 ; (From wildcard) Psi prime peptides AA CM CM CT OH 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) allyl alcohols, ethers CM CM CT OS 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; (From wildcard) allyl alcohols, ethers CT C= C OH 3 1.78866 -5.05218 -0.96232 4.22584 0.00000 0.00000 ; (From wildcard) 2-Me-1,3-butadiene-like CT C= C O 3 1.78866 -5.05218 -0.96232 4.22584 0.00000 0.00000 ; (From wildcard) 2-Me-1,3-butadiene-like CT C= C O_3 3 1.78866 -5.05218 -0.96232 4.22584 0.00000 0.00000 ; (From wildcard) 2-Me-1,3-butadiene-like CT C= C O_2 3 1.78866 -5.05218 -0.96232 4.22584 0.00000 0.00000 ; (From wildcard) 2-Me-1,3-butadiene-like CT CM C OH 3 1.78866 -5.05218 -0.96232 4.22584 0.00000 0.00000 ; (From wildcard) 2-Me-1,3-butadiene-like CT CM C O 3 1.78866 -5.05218 -0.96232 4.22584 0.00000 0.00000 ; (From wildcard) 2-Me-1,3-butadiene-like CT CM C O_3 3 1.78866 -5.05218 -0.96232 4.22584 0.00000 0.00000 ; (From wildcard) 2-Me-1,3-butadiene-like CT CM C O_2 3 1.78866 -5.05218 -0.96232 4.22584 0.00000 0.00000 ; (From wildcard) 2-Me-1,3-butadiene-like HA CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) H4 CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CT CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CT CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CT CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CT CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CA CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CA CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CA CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CA CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C! CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C! CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C! CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C! CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_2 CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_2 CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_2 CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_2 CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_3 CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_3 CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_3 CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_3 CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C* CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C* CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C* CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CV CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CV CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CV CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CV CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CW CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CW CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CW CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CW CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CS CW NA CT 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CS CW NA CN 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CS CW NA CR 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CS CW NA CW 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CT CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CA CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C! CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_2 CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C_3 CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) C* CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CV CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CW CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CS CW NA NB 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CT NA CW HA 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CT NA CW H4 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CN NA CW H4 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CR NA CW H4 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CW NA CW HA 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CW NA CW H4 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; (From wildcard) CT NA CR NC 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CT NA CR NA 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CT NA CR NB 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CB NA CR NC 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CB NA CR NA 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CB NA CR NB 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CW NA CR NC 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CW NA CR NA 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CX NA CR NC 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CX NA CR NB 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; (From wildcard) CT CT NT CA 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CT CT NT C 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CT CT NT C_2 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CT CT NT C_3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CT CT NT C3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CA CT NT CA 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CA CT NT C 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CA CT NT C_2 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CA CT NT C_3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CA CT NT C3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C CT NT CA 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C CT NT C 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C CT NT C_2 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C CT NT C_3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C CT NT C3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_2 CT NT CA 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_2 CT NT C 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_2 CT NT C_2 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_2 CT NT C_3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_2 CT NT C3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_3 CT NT CA 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_3 CT NT C 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_3 CT NT C_2 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_3 CT NT C_3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C_3 CT NT C3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C3 CT NT CA 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C3 CT NT C 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C3 CT NT C_2 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C3 CT NT C_3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom C3 CT NT C3 3 1.78866 3.49154 0.53555 -5.81576 0.00000 0.00000 ; (From wildcard) amine all-atom CA CA N X 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; N-phenylamide CT CT CK X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CA CA CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; ethyl benzene NZ CZ CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; nitriles O C CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides CT CT C* X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CQ X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CR X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CS X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CU X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CT CT CV X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics OY SY N X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY C3 X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY CA X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY OY X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY NT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide OY SY CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide CT CT CW X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics CZ CZ CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; alkynes Cl CT CS X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; chloromethyl aromatic Cl CT CW X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; chloromethyl aromatic F CT CS X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; fluoromethyl aromatic H N CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides F CT CW X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; fluoromethyl aromatic H N CT_2 X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; peptides H-N-CA-X H N2 CA X 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline-like H N2 CQ X 3 8.49352 0.00000 -8.49352 0.00000 0.00000 0.00000 ; aniline-like H NA CB X 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; H NA CR X 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; H NA CW X 3 13.38880 0.00000 -13.38880 0.00000 0.00000 0.00000 ; HA CR NA X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; HC CT C* X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CK X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CQ X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CR X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CS X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CU X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CV X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics HC CT CW X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; aromatics N SY CT X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; sulfonamide X C CB X 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; X C CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X C* CB X 3 14.01640 0.00000 -14.01640 0.00000 0.00000 0.00000 ; X C* CW X 3 54.60120 0.00000 -54.60120 0.00000 0.00000 0.00000 ; X CA S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with S X CA CA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA CB X 3 29.28800 0.00000 -29.28800 0.00000 0.00000 0.00000 ; X CA CN X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CA CR X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA CU X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA CW X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CA OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with O X CB N X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CB CB X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CB CN X 3 25.10400 0.00000 -25.10400 0.00000 0.00000 0.00000 ; X CB CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CB NA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CB NB X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CB NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CK NA X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CK NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CK NC X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CM CM X 3 58.57600 0.00000 -58.57600 0.00000 0.00000 0.00000 ; alkene X CN NA X 3 12.76120 0.00000 -12.76120 0.00000 0.00000 0.00000 ; X CQ N X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CQ NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CR S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring thiazole X CR CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CR NA X 3 19.45560 0.00000 -19.45560 0.00000 0.00000 0.00000 ; X CR NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CR NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; X CR OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring oxazole X CS CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CS CW X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CU NB X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CV CW X 3 44.97800 0.00000 -44.97800 0.00000 0.00000 0.00000 ; X CV NA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X CV NB X 3 20.08320 0.00000 -20.08320 0.00000 0.00000 0.00000 ; X CW S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring thiazole X CW CW X 3 44.97800 0.00000 -44.97800 0.00000 0.00000 0.00000 ; X CW NA X 3 11.71520 0.00000 -11.71520 0.00000 0.00000 0.00000 ; X CW NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X CW OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring furan X CY S X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; small ring X CY CY X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; small ring X CZ CZ X 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; alkynes X NA S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with S X NA NB X 3 41.84000 0.00000 -41.84000 0.00000 0.00000 0.00000 ; X NA OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with O X NB OS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring isoxazole X NC NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring X OS S X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring with S X CX CX X 3 44.97800 0.00000 -44.97800 0.00000 0.00000 0.00000 ; ; Residue-specific sidechain dihedrals, and sidechain acids. Use explicitly in rtp or top files. ; Chi-1 N-C-C-O in SER & THR #define dih_SER_THR_chi1_N_C_C_O 9.89307 -4.71746 3.67774 -8.85335 0.00000 0.00000 ; Chi-1 CO-C-C-O in SER & THR #define dih_SER_THR_chi1_CO_C_C_O -15.47661 11.82816 3.64845 0.00000 0.00000 0.00000 ; Chi-2 C-C-OH-OH in SER & THR #define dih_SER_THR_chi2_C_C_OH_HO -4.16308 6.71114 3.63590 -6.18395 0.00000 0.00000 ; Chi-1 N-C-C-S in CYS & CYX #define dih_CYS_chi1_N_C_C_S 3.40787 -2.80537 -0.35982 -0.24267 0.00000 0.00000 ; Chi-1 CO-C-C-S in CYS & CYX #define dih_CYS_chi1_CO_C_C_S -16.25902 9.08765 7.17138 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in ASN #define dih_ASN_chi1_N_C_C_C -7.02075 16.44730 2.83256 -12.25912 0.00000 0.00000 ; Chi-1 C-C-C-CO in ASN #define dih_ASN_chi1_C_C_C_CO -4.52081 -2.18614 6.70695 0.00000 0.00000 0.00000 ; Chi-2 C-C-CO-N in ASN #define dih_ASN_chi2_C_C_CO_N -9.49768 -6.36386 8.89936 6.96218 0.00000 0.00000 ; Chi-1 N-C-C-C in GLN #define dih_GLN_chi1_N_C_C_C 1.92464 2.61081 2.20079 -6.73624 0.00000 0.00000 ; Chi-1 C-C-C-CO in GLN #define dih_GLN_chi1_C_C_C_CO -2.13384 5.63166 -3.49782 0.00000 0.00000 0.00000 ; Chi-3 C-C-CO-N in GLN #define dih_GLN_chi3_C_C_CO_N 6.64001 -10.55205 -10.96626 14.87830 0.00000 0.00000 ; Chi-1 N-C-C-C in HIS (HID & HIE) #define dih_HIS_chi1_N_C_C_C 1.21336 3.30536 -2.10036 -2.41835 0.00000 0.00000 ; Chi-1 C-C-C-CO in HIS (HID & HIE) #define dih_HIS_chi1_C_C_C_CO -3.16938 3.36184 -0.19246 0.00000 0.00000 0.00000 ; Chi-2 C-C-C-N in HIS (HID & HIE) #define dih_HIS_chi2_C_C_C_N 0.38702 5.52916 -0.05858 -5.85760 0.00000 0.00000 ; Chi-1 N-C-C-C in HIP #define dih_HIP_chi1_N_C_C_C 2.33258 8.48724 1.46440 -12.28422 0.00000 0.00000 ; Chi-1 C-C-C-CO in HIP #define dih_HIP_chi1_C_C_C_CO 3.85556 -3.51247 -0.34309 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in LEU #define dih_LEU_chi1_N_C_C_C 2.57316 3.49782 -1.10039 -4.97059 0.00000 0.00000 ; Chi-1 C-C-C-CO in LEU #define dih_LEU_chi1_C_C_C_CO -0.82216 1.12759 -0.30544 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in VAL #define dih_VAL_chi1_N_C_C_C 4.50199 0.78241 -1.60247 -3.68192 0.00000 0.00000 ; Chi-1 C-C-C-CO in VAL #define dih_VAL_chi1_C_C_C_CO 0.42259 2.70705 -3.12964 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in ILE #define dih_ILE_chi1_N_C_C_C 10.62108 -2.26146 -3.99154 -4.36810 0.00000 0.00000 ; Chi-1 C-C-C-CO in ILE #define dih_ILE_chi1_C_C_C_CO 6.75716 -1.41838 -5.33879 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in MET #define dih_MET_chi1_N_C_C_C 3.75096 -3.73841 -0.83261 0.82006 0.00000 0.00000 ; Chi-1 C-C-C-CO in MET #define dih_MET_chi1_C_C_C_CO -2.38488 -0.80333 3.18821 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in TRP #define dih_TRP_chi1_N_C_C_C -0.15899 3.29699 -2.35141 -0.78659 0.00000 0.00000 ; Chi-1 C-C-C-CO in TRP #define dih_TRP_chi1_C_C_C_CO -4.82834 2.21334 2.61500 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in ASP #define dih_ASP_chi1_N_C_C_C -6.01868 7.57513 -4.00827 2.45182 0.00000 0.00000 ; Chi-1 C-C-C-CO in ASP #define dih_ASP_chi1_C_C_C_CO 8.67552 4.30743 -12.98295 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in GLU #define dih_GLU_chi1_N_C_C_C 8.79268 -11.83444 1.07529 1.96648 0.00000 0.00000 ; Chi-1 C-C-C-CO in GLU #define dih_GLU_chi1_C_C_C_CO -5.77392 3.38485 2.38906 0.00000 0.00000 0.00000 ; Chi-1 N-C-C-C in LYS #define dih_LYS_chi1_N_C_C_C 1.27612 1.16734 0.89538 -3.33884 0.00000 0.00000 ; Chi-1 C-C-C-CO in LYS #define dih_LYS_chi1_C_C_C_CO -6.91824 4.67562 2.24262 0.00000 0.00000 0.00000 ; Chi-5 C-C-N-H in LYSH #define dih_LYS_chi5_C_C_N_H 0.72592 2.17777 0.00000 -2.90370 0.00000 0.00000 ; Chi-1 N-C-C-C in ARG #define dih_ARG_chi1_N_C_C_C 10.23197 3.52083 -3.97899 -9.77382 0.00000 0.00000 ; Chi-1 C-C-C-CO in ARG #define dih_ARG_chi1_C_C_C_CO 5.49778 1.41838 -6.91615 0.00000 0.00000 0.00000 ; Sidechain RCOOH acid (GLUH and ASPH), O=C-OH-HO dihedral #define dih_sidechain_COOH_O_C_O_H 20.50160 0.00000 -20.50160 0.00000 0.00000 0.00000 ; Sidechain RCOOH acid (GLUH and ASPH), CT-C-OH-HO dihedral #define dih_sidechain_COOH_C_C_O_H 26.77760 -6.27600 -20.50160 0.00000 0.00000 0.00000 ; Below are extra dihedrals for some special organic molecules. ; Since the atom types are identical to other dihedrals you have to specify ; them explicitly with a define if you happen to simulate this type of molecule. ; CT-C-OH-HO in 1,2-diacid monoanion #define dih_diacid_CT_C_OH_HO 27.19600 -6.69440 -20.50160 0.00000 0.00000 0.00000 ; CT-CT-C-O in 1,2-diacid monoanion #define dih_diacid_CT_CT_C_O -11.92440 -3.55640 7.94960 7.53120 0.00000 0.00000 ; CT-CT-CT-CT in perfluoroalkanes #define dih_perfluoroalkane_CT_CT_CT_CT 14.91596 -22.56431 -39.41328 11.61479 35.44685 0.00000 ; CT-CT-NT-CT in exocyclic 1,4-diamines #define dih_exo_diamines_CT_CT_NT_CT 3.98108 1.29913 0.53555 -5.81576 0.00000 0.00000 ; CT-CT-NT-CT in exocyclic amines #define dih_exo_amines_CT_CT_NT_CT 4.13170 1.14851 0.53555 -5.81576 0.00000 0.00000 ; CT-CT-NT-H in azetidine / 4 membered cyclic amines #define dih_azetidine_CT_CT_NT_H 16.73600 0.00000 -16.73600 0.00000 0.00000 0.00000 ; CT-CT-NT-H in pyrrolidine / 5 membered cyclic amines #define dih_pyrrolidine_CT_CT_NT_H -0.45187 2.20496 1.74473 -3.49782 0.00000 0.00000 ; CT-CT-NT-H in cyclic amines #define dih_cyclic_amines_CT_CT_NT_H 0.84308 0.91002 1.74473 -3.49782 0.00000 0.00000 ; CT-CT-NT-H in cyclic 1,4-diamines #define dih_cyclic_diamines_CT_CT_NT_H 2.31375 -0.56065 1.74473 -3.49782 0.00000 0.00000 ; HC-C-C-O in dicarbonyls #define dih_carbonyls_HC_C_C_O 0.83680 0.00000 -0.83680 0.00000 0.00000 0.00000 ; OH-CT-CT-OH in diols #define dih_diols_OH_CT_CT_OH 19.89074 -19.89074 0.00000 0.00000 0.00000 0.00000 ; OH-CT-CT-OH in triols #define dih_triols_OH_CT_CT_OH 25.59353 -25.59353 0.00000 0.00000 0.00000 0.00000 ; CT-CT-CT-OH in polyols #define dih_polyols_CT_CT_CT_OH -3.24679 3.24679 0.00000 0.00000 0.00000 0.00000 ; CT-CT-OH-HO in hexopyranoses #define dih_hexopyranoses_CT_CT_OH_HO -4.32207 0.84516 12.06247 -8.58556 0.00000 0.00000 ; CT-CT-CT-O? in hexopyranoses #define dih_hexopyranoses_CT_CT_CT_O -2.79491 2.79491 0.00000 0.00000 0.00000 0.00000 ; C-CT-CT-C in dicarboxylic acid #define dih_dicarboxylicacid_C_CT_CT_C 0.94140 7.42660 0.00000 -8.36800 0.00000 0.00000 ; O-C-OH-HO in dicarboxylic acid #define dih_dicarboxylicacid_O_C_OH_HO 23.01200 0.00000 -23.01200 0.00000 0.00000 0.00000 ; CT-C-OH-HO in dicarboxylic acid #define dih_dicarboxylicacid_CT_C_OH_HO 26.15000 -3.13800 -23.01200 0.00000 0.00000 0.00000 ; HC-C-OH-HO in dicarboxylic acid #define dih_dicarboxylicacid_HC_C_OH_HO 26.15000 -3.13800 -23.01200 0.00000 0.00000 0.00000 ; C-CT-CT-HC in dicarboxylic acid #define dih_dicarboxylicacid_C_CT_CT_HC 0.15481 0.46442 0.00000 -0.61924 0.00000 0.00000 ; CT-CT-C-O in dicarboxylic acid #define dih_dicarboxylicacid_CT_CT_C_O -4.39320 0.00000 2.30120 2.09200 0.00000 0.00000 ; C-CT-C-OH in dicarboxylic acid #define dih_dicarboxylicacid_CT_CT_C_OH 5.90781 0.00000 -5.90781 0.00000 0.00000 0.00000 [ dihedraltypes ] ; Improper OPLS dihedrals to keep groups planar. ; (OPLS doesnt use impropers for chiral atoms). ; Since these functions are periodic of the form 1-cos(2*x), they are actually ; implemented as proper dihedrals [1+cos(2*x+180)] for the moment, ; to keep things compatible. ; The defines are used in ffoplsaa.rtp or directly in your .top file. ; O?-C -X -Y improper torsion. C can be C_2 or C_3 too. #define improper_O_C_X_Y 180.0 43.93200 2 ; X-NO-ON-NO improper torsion. #define improper_X_NO_ON_NO 180.0 43.93200 2 ; N2-X-N2-N2 improper torsion. #define improper_N2_X_N2_N2 180.0 43.93200 2 ; Z -N?-X -Y improper torsion #define improper_Z_N_X_Y 180.0 4.18400 2 ; Z -CM-X -Y improper torsion. CM can be C= too. #define improper_Z_CM_X_Y 180.0 62.76000 2 ; Z -CA-X -Y improper torsion. CA is any ring carbon (CA,CB,CN,CV,CW,CR,CK,CQ,CS,C*) #define improper_Z_CA_X_Y 180.0 4.60240 2 ; ; This bit added by DvdS for quartz simulation 2005-05-07 ; These parameters are taken from GROMOS and were also used in ; Wensink et al. Langmuir 16 (2000) pp. 7392-7400 ; [ bondtypes ] ; i j func b0 kb SI OS 1 0.16300 251040. ; From GROMACS SI OH 1 0.16300 251040. ; [ angletypes ] ; i j k func th0 cth SI OS SI 1 155.000 397.480 OS SI OS 1 109.500 397.480 OH SI OS 1 109.500 397.480 SI OH HO 1 109.500 397.480 [ dihedraltypes ] ; i j k l func coefficients ; Added DvdS for Quartz simulations SI OS 1 0.000 3.766 3 SI OH 1 0.000 3.766 3 ; Added by DvdS for DMSO 17/06/2006 [ bondtypes ] O2 S 1 0.153 400000 [ angletypes ] O2 S CT 1 107 400 [ dihedraltypes ] O2 S CT HC 3 1.35352 4.06057 0.00000 -5.41410 0.00000 0.00000 ; sulfide all-atom
--2021-05-28 01:00:48-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro
Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro [following]
--2021-05-28 01:00:48-- https://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 399
Saving to: `etane.gro'
0K 100% 5,51M=0s
2021-05-28 01:00:49 (5,51 MB/s) - `etane.gro' saved [399/399]
Конфигурации контроля температуры¶
- метод Берендсена
- Velocity rescale
- метод Нуза-Хувера
- метод Андерсена
- метод стохастической МД
In [3]:
%%bash
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp
--2021-05-28 01:01:18-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp [following]
--2021-05-28 01:01:18-- https://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1356 (1,3K)
Saving to: `be.mdp'
0K . 100% 14,8M=0s
2021-05-28 01:01:19 (14,8 MB/s) - `be.mdp' saved [1356/1356]
--2021-05-28 01:01:19-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp
Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp [following]
--2021-05-28 01:01:19-- https://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1427 (1,4K)
Saving to: `vr.mdp'
0K . 100% 14,8M=0s
2021-05-28 01:01:20 (14,8 MB/s) - `vr.mdp' saved [1427/1427]
--2021-05-28 01:01:20-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp
Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp [following]
--2021-05-28 01:01:20-- https://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1429 (1,4K)
Saving to: `nh.mdp'
0K . 100% 15,3M=0s
2021-05-28 01:01:21 (15,3 MB/s) - `nh.mdp' saved [1429/1429]
--2021-05-28 01:01:21-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp
Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp [following]
--2021-05-28 01:01:21-- https://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1426 (1,4K)
Saving to: `an.mdp'
0K . 100% 13,9M=0s
2021-05-28 01:01:22 (13,9 MB/s) - `an.mdp' saved [1426/1426]
--2021-05-28 01:01:22-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp
Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp [following]
--2021-05-28 01:01:22-- https://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp
Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1441 (1,4K)
Saving to: `sd.mdp'
0K . 100% 15,2M=0s
2021-05-28 01:01:23 (15,2 MB/s) - `sd.mdp' saved [1441/1441]
Исправленный top файл¶
In [5]:
!cat et.top
#include "/usr/share/gromacs/top/oplsaa.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl et 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_135 1 ETH C1 1 -0.189 12.01 2 opls_135 1 ETH C2 2 -0.155 12.01 3 opls_140 1 ETH H1 3 0.0059 1.008 4 opls_140 1 ETH H2 4 0.0059 1.008 5 opls_140 1 ETH H3 5 0.0059 1.008 6 opls_140 1 ETH H4 6 0.0056 1.008 7 opls_140 1 ETH H5 7 0.0056 1.008 8 opls_140 1 ETH H6 8 0.0056 1.008 [ bonds ] ; ai aj funct b0 kb 1 2 1 1 3 1 1 4 1 1 5 1 2 6 1 2 7 1 2 8 1 [ angles ] ; ai aj ak funct phi0 kphi ;around c1 3 1 4 1 4 1 5 1 3 1 5 1 2 1 3 1 2 1 4 1 2 1 5 1 ;around c2 1 2 6 1 1 2 7 1 1 2 8 1 6 2 7 1 6 2 8 1 7 2 8 1 [ dihedrals ] ; ai aj ak al funct 3 1 2 6 3 3 1 2 7 3 3 1 2 8 3 4 1 2 6 3 4 1 2 7 3 4 1 2 8 3 5 1 2 6 3 5 1 2 7 3 5 1 2 8 3 [ pairs ] ; list of atoms 1-4 ; ai aj funct 3 6 3 7 3 8 4 6 4 7 4 8 5 6 5 7 5 8 [ System ] ; any text here first one [ molecules ] ;Name count et 1
Создание входных данных¶
In [6]:
from glob import glob
mdps = [x for x in glob("./*.mdp")]
In [34]:
for f in mdps:
prefix = f.split(".")[-2].split("/")[-1]
f1 = f.replace("mdp", "tpr")
f2 = f.replace("mdp", "trr")
f3 = f.replace("mdp", "pdb")
! grompp -f {f} -c etane.gro -p et.top -o {f1}
! mdrun -deffnm {prefix} -v -nt 1
! echo 0 | trjconv -f {f2} -s {f1} -o {f3}
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f ./be.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c etane.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o ./be.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
NOTE 1 [file ./be.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file ./be.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 3 [file et.top, line 68]:
System has non-zero total charge: -0.309500
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 4 [file ./be.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 8 Mb of data
There were 4 notes
Back Off! I just backed up ./be.tpr to ./#be.tpr.3#
gcq#201: "Beat On the Brat With a Baseball Bat" (The Ramones)
:-) G R O M A C S (-:
Glycine aRginine prOline Methionine Alanine Cystine Serine
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s be.tpr Input Run input file: tpr tpb tpa
-o be.trr Output Full precision trajectory: trr trj cpt
-x be.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi be.cpt Input, Opt. Checkpoint file
-cpo be.cpt Output, Opt. Checkpoint file
-c be.gro Output Structure file: gro g96 pdb etc.
-e be.edr Output Energy file
-g be.log Output Log file
-dhdl be.xvg Output, Opt. xvgr/xmgr file
-field be.xvg Output, Opt. xvgr/xmgr file
-table be.xvg Input, Opt. xvgr/xmgr file
-tablep be.xvg Input, Opt. xvgr/xmgr file
-tableb be.xvg Input, Opt. xvgr/xmgr file
-rerun be.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi be.xvg Output, Opt. xvgr/xmgr file
-tpid be.xvg Output, Opt. xvgr/xmgr file
-ei be.edi Input, Opt. ED sampling input
-eo be.edo Output, Opt. ED sampling output
-j be.gct Input, Opt. General coupling stuff
-jo be.gct Output, Opt. General coupling stuff
-ffout be.xvg Output, Opt. xvgr/xmgr file
-devout be.xvg Output, Opt. xvgr/xmgr file
-runav be.xvg Output, Opt. xvgr/xmgr file
-px be.xvg Output, Opt. xvgr/xmgr file
-pf be.xvg Output, Opt. xvgr/xmgr file
-mtx be.mtx Output, Opt. Hessian matrix
-dn be.ndx Output, Opt. Index file
-multidir be Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string be Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up be.log to ./#be.log.2#
Getting Loaded...
Reading file be.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up be.trr to ./#be.trr.2#
Back Off! I just backed up be.edr to ./#be.edr.2#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up be.gro to ./#be.gro.2#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.820 4.123 92.7
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 390.723 5654.473 0.004
gcq#44: "You Try to Run the Universe" (Tricky)
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f ./be.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o ./be.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s ./be.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-[no]round bool no Round measurements to nearest picosecond
-dump time -1 Dump frame nearest specified time (ps)
-t0 time 0 Starting time (ps) (default: don't change)
-timestep time 0 Change time step between input frames (ps)
-pbc enum none PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-clustercenter vector 0 0 0 Optional starting point for pbc cluster option
-trans vector 0 0 0 All coordinates will be translated by trans. This
can advantageously be combined with -pbc mol -ur
compact.
-shift vector 0 0 0 All coordinates will be shifted by framenr*shift
-fit enum none Fit molecule to ref structure in the structure
file: none, rot+trans, rotxy+transxy,
translation, transxy or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool no Read and write forces if possible
-trunc time -1 Truncate input trajectory file after this time
(ps)
-exec string Execute command for every output frame with the
frame number as argument
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb
file
-nzero int 0 If the -sep flag is set, use these many digits
for the file numbers and prepend zeros as needed
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
-[no]conect bool no Add conect records when writing .pdb files.
Useful for visualization of non-standard
molecules, e.g. coarse grained ones
Will write pdb: Protein data bank file
Reading file ./be.tpr, VERSION 4.5.5 (single precision)
Reading file ./be.tpr, VERSION 4.5.5 (single precision)
Select group for output
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group: Selected 0: 'System'
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up ./be.pdb to ./#be.pdb.2#
-> frame 250 time 250.000 -> frame 200 time 200.000
gcq#44: "You Try to Run the Universe" (Tricky)
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f ./vr.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c etane.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o ./vr.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
NOTE 1 [file ./vr.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 2 [file et.top, line 68]:
System has non-zero total charge: -0.309500
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 3 [file ./vr.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 8 Mb of data
There were 3 notes
Back Off! I just backed up ./vr.tpr to ./#vr.tpr.1#
gcq#44: "You Try to Run the Universe" (Tricky)
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s vr.tpr Input Run input file: tpr tpb tpa
-o vr.trr Output Full precision trajectory: trr trj cpt
-x vr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi vr.cpt Input, Opt. Checkpoint file
-cpo vr.cpt Output, Opt. Checkpoint file
-c vr.gro Output Structure file: gro g96 pdb etc.
-e vr.edr Output Energy file
-g vr.log Output Log file
-dhdl vr.xvg Output, Opt. xvgr/xmgr file
-field vr.xvg Output, Opt. xvgr/xmgr file
-table vr.xvg Input, Opt. xvgr/xmgr file
-tablep vr.xvg Input, Opt. xvgr/xmgr file
-tableb vr.xvg Input, Opt. xvgr/xmgr file
-rerun vr.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi vr.xvg Output, Opt. xvgr/xmgr file
-tpid vr.xvg Output, Opt. xvgr/xmgr file
-ei vr.edi Input, Opt. ED sampling input
-eo vr.edo Output, Opt. ED sampling output
-j vr.gct Input, Opt. General coupling stuff
-jo vr.gct Output, Opt. General coupling stuff
-ffout vr.xvg Output, Opt. xvgr/xmgr file
-devout vr.xvg Output, Opt. xvgr/xmgr file
-runav vr.xvg Output, Opt. xvgr/xmgr file
-px vr.xvg Output, Opt. xvgr/xmgr file
-pf vr.xvg Output, Opt. xvgr/xmgr file
-mtx vr.mtx Output, Opt. Hessian matrix
-dn vr.ndx Output, Opt. Index file
-multidir vr Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string vr Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file vr.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.890 4.168 93.3
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 383.701 5552.722 0.004
gcq#253: "Disturb the Peace of a John Q Citizen" (Urban Dance Squad)
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f ./vr.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o ./vr.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s ./vr.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-[no]round bool no Round measurements to nearest picosecond
-dump time -1 Dump frame nearest specified time (ps)
-t0 time 0 Starting time (ps) (default: don't change)
-timestep time 0 Change time step between input frames (ps)
-pbc enum none PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-clustercenter vector 0 0 0 Optional starting point for pbc cluster option
-trans vector 0 0 0 All coordinates will be translated by trans. This
can advantageously be combined with -pbc mol -ur
compact.
-shift vector 0 0 0 All coordinates will be shifted by framenr*shift
-fit enum none Fit molecule to ref structure in the structure
file: none, rot+trans, rotxy+transxy,
translation, transxy or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool no Read and write forces if possible
-trunc time -1 Truncate input trajectory file after this time
(ps)
-exec string Execute command for every output frame with the
frame number as argument
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb
file
-nzero int 0 If the -sep flag is set, use these many digits
for the file numbers and prepend zeros as needed
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
-[no]conect bool no Add conect records when writing .pdb files.
Useful for visualization of non-standard
molecules, e.g. coarse grained ones
Will write pdb: Protein data bank file
Reading file ./vr.tpr, VERSION 4.5.5 (single precision)
Reading file ./vr.tpr, VERSION 4.5.5 (single precision)
Select group for output
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group: Selected 0: 'System'
trn version: GMX_trn_file (single precision)
-> frame 250 time 250.000 -> frame 200 time 200.000
gcq#253: "Disturb the Peace of a John Q Citizen" (Urban Dance Squad)
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f ./nh.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c etane.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o ./nh.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
NOTE 1 [file ./nh.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file ./nh.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 3 [file et.top, line 68]:
System has non-zero total charge: -0.309500
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 4 [file ./nh.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 8 Mb of data
There were 4 notes
Back Off! I just backed up ./nh.tpr to ./#nh.tpr.1#
gcq#253: "Disturb the Peace of a John Q Citizen" (Urban Dance Squad)
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s nh.tpr Input Run input file: tpr tpb tpa
-o nh.trr Output Full precision trajectory: trr trj cpt
-x nh.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi nh.cpt Input, Opt. Checkpoint file
-cpo nh.cpt Output, Opt. Checkpoint file
-c nh.gro Output Structure file: gro g96 pdb etc.
-e nh.edr Output Energy file
-g nh.log Output Log file
-dhdl nh.xvg Output, Opt. xvgr/xmgr file
-field nh.xvg Output, Opt. xvgr/xmgr file
-table nh.xvg Input, Opt. xvgr/xmgr file
-tablep nh.xvg Input, Opt. xvgr/xmgr file
-tableb nh.xvg Input, Opt. xvgr/xmgr file
-rerun nh.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi nh.xvg Output, Opt. xvgr/xmgr file
-tpid nh.xvg Output, Opt. xvgr/xmgr file
-ei nh.edi Input, Opt. ED sampling input
-eo nh.edo Output, Opt. ED sampling output
-j nh.gct Input, Opt. General coupling stuff
-jo nh.gct Output, Opt. General coupling stuff
-ffout nh.xvg Output, Opt. xvgr/xmgr file
-devout nh.xvg Output, Opt. xvgr/xmgr file
-runav nh.xvg Output, Opt. xvgr/xmgr file
-px nh.xvg Output, Opt. xvgr/xmgr file
-pf nh.xvg Output, Opt. xvgr/xmgr file
-mtx nh.mtx Output, Opt. Hessian matrix
-dn nh.ndx Output, Opt. Index file
-multidir nh Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string nh Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file nh.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.880 4.112 94.4
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 384.673 5567.033 0.004
gcq#96: "Proceed, With Fingers Crossed" (TeX)
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f ./nh.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o ./nh.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s ./nh.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-[no]round bool no Round measurements to nearest picosecond
-dump time -1 Dump frame nearest specified time (ps)
-t0 time 0 Starting time (ps) (default: don't change)
-timestep time 0 Change time step between input frames (ps)
-pbc enum none PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-clustercenter vector 0 0 0 Optional starting point for pbc cluster option
-trans vector 0 0 0 All coordinates will be translated by trans. This
can advantageously be combined with -pbc mol -ur
compact.
-shift vector 0 0 0 All coordinates will be shifted by framenr*shift
-fit enum none Fit molecule to ref structure in the structure
file: none, rot+trans, rotxy+transxy,
translation, transxy or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool no Read and write forces if possible
-trunc time -1 Truncate input trajectory file after this time
(ps)
-exec string Execute command for every output frame with the
frame number as argument
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb
file
-nzero int 0 If the -sep flag is set, use these many digits
for the file numbers and prepend zeros as needed
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
-[no]conect bool no Add conect records when writing .pdb files.
Useful for visualization of non-standard
molecules, e.g. coarse grained ones
Will write pdb: Protein data bank file
Reading file ./nh.tpr, VERSION 4.5.5 (single precision)
Reading file ./nh.tpr, VERSION 4.5.5 (single precision)
Select group for output
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group: Selected 0: 'System'
trn version: GMX_trn_file (single precision)
-> frame 250 time 250.000 -> frame 200 time 200.000
gcq#96: "Proceed, With Fingers Crossed" (TeX)
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f ./an.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c etane.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o ./an.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
NOTE 1 [file ./an.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 2 [file et.top, line 68]:
System has non-zero total charge: -0.309500
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 3 [file ./an.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 8 Mb of data
There were 3 notes
Back Off! I just backed up ./an.tpr to ./#an.tpr.1#
gcq#96: "Proceed, With Fingers Crossed" (TeX)
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s an.tpr Input Run input file: tpr tpb tpa
-o an.trr Output Full precision trajectory: trr trj cpt
-x an.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi an.cpt Input, Opt. Checkpoint file
-cpo an.cpt Output, Opt. Checkpoint file
-c an.gro Output Structure file: gro g96 pdb etc.
-e an.edr Output Energy file
-g an.log Output Log file
-dhdl an.xvg Output, Opt. xvgr/xmgr file
-field an.xvg Output, Opt. xvgr/xmgr file
-table an.xvg Input, Opt. xvgr/xmgr file
-tablep an.xvg Input, Opt. xvgr/xmgr file
-tableb an.xvg Input, Opt. xvgr/xmgr file
-rerun an.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi an.xvg Output, Opt. xvgr/xmgr file
-tpid an.xvg Output, Opt. xvgr/xmgr file
-ei an.edi Input, Opt. ED sampling input
-eo an.edo Output, Opt. ED sampling output
-j an.gct Input, Opt. General coupling stuff
-jo an.gct Output, Opt. General coupling stuff
-ffout an.xvg Output, Opt. xvgr/xmgr file
-devout an.xvg Output, Opt. xvgr/xmgr file
-runav an.xvg Output, Opt. xvgr/xmgr file
-px an.xvg Output, Opt. xvgr/xmgr file
-pf an.xvg Output, Opt. xvgr/xmgr file
-mtx an.mtx Output, Opt. Hessian matrix
-dn an.ndx Output, Opt. Index file
-multidir an Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string an Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file an.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.800 4.048 93.9
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 392.930 5684.234 0.004
gcq#190: "Load Up Your Rubber Bullets" (10 CC)
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f ./an.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o ./an.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s ./an.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-[no]round bool no Round measurements to nearest picosecond
-dump time -1 Dump frame nearest specified time (ps)
-t0 time 0 Starting time (ps) (default: don't change)
-timestep time 0 Change time step between input frames (ps)
-pbc enum none PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-clustercenter vector 0 0 0 Optional starting point for pbc cluster option
-trans vector 0 0 0 All coordinates will be translated by trans. This
can advantageously be combined with -pbc mol -ur
compact.
-shift vector 0 0 0 All coordinates will be shifted by framenr*shift
-fit enum none Fit molecule to ref structure in the structure
file: none, rot+trans, rotxy+transxy,
translation, transxy or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool no Read and write forces if possible
-trunc time -1 Truncate input trajectory file after this time
(ps)
-exec string Execute command for every output frame with the
frame number as argument
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb
file
-nzero int 0 If the -sep flag is set, use these many digits
for the file numbers and prepend zeros as needed
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
-[no]conect bool no Add conect records when writing .pdb files.
Useful for visualization of non-standard
molecules, e.g. coarse grained ones
Will write pdb: Protein data bank file
Reading file ./an.tpr, VERSION 4.5.5 (single precision)
Reading file ./an.tpr, VERSION 4.5.5 (single precision)
Select group for output
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group: Selected 0: 'System'
trn version: GMX_trn_file (single precision)
-> frame 250 time 250.000 -> frame 200 time 200.000
gcq#305: "Shoot them in the back now" (The Ramones)
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f ./sd.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c etane.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p et.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o ./sd.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
NOTE 1 [file ./sd.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Setting the LD random seed to 11892
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'et'
NOTE 2 [file et.top, line 68]:
System has non-zero total charge: -0.309500
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group System is 21.00
NOTE 3 [file ./sd.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 8 Mb of data
There were 3 notes
Back Off! I just backed up ./sd.tpr to ./#sd.tpr.1#
gcq#305: "Shoot them in the back now" (The Ramones)
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s sd.tpr Input Run input file: tpr tpb tpa
-o sd.trr Output Full precision trajectory: trr trj cpt
-x sd.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi sd.cpt Input, Opt. Checkpoint file
-cpo sd.cpt Output, Opt. Checkpoint file
-c sd.gro Output Structure file: gro g96 pdb etc.
-e sd.edr Output Energy file
-g sd.log Output Log file
-dhdl sd.xvg Output, Opt. xvgr/xmgr file
-field sd.xvg Output, Opt. xvgr/xmgr file
-table sd.xvg Input, Opt. xvgr/xmgr file
-tablep sd.xvg Input, Opt. xvgr/xmgr file
-tableb sd.xvg Input, Opt. xvgr/xmgr file
-rerun sd.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi sd.xvg Output, Opt. xvgr/xmgr file
-tpid sd.xvg Output, Opt. xvgr/xmgr file
-ei sd.edi Input, Opt. ED sampling input
-eo sd.edo Output, Opt. ED sampling output
-j sd.gct Input, Opt. General coupling stuff
-jo sd.gct Output, Opt. General coupling stuff
-ffout sd.xvg Output, Opt. xvgr/xmgr file
-devout sd.xvg Output, Opt. xvgr/xmgr file
-runav sd.xvg Output, Opt. xvgr/xmgr file
-px sd.xvg Output, Opt. xvgr/xmgr file
-pf sd.xvg Output, Opt. xvgr/xmgr file
-mtx sd.mtx Output, Opt. Hessian matrix
-dn sd.ndx Output, Opt. Index file
-multidir sd Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string sd Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file sd.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s remaining runtime: 3 s
Writing final coordinates.
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 4.470 4.778 93.6
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 349.058 4832.234 0.005
gcq#148: "Everybody's Good Enough For Some Change" (LIVE)
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f ./sd.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-o ./sd.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s ./sd.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-[no]round bool no Round measurements to nearest picosecond
-dump time -1 Dump frame nearest specified time (ps)
-t0 time 0 Starting time (ps) (default: don't change)
-timestep time 0 Change time step between input frames (ps)
-pbc enum none PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-clustercenter vector 0 0 0 Optional starting point for pbc cluster option
-trans vector 0 0 0 All coordinates will be translated by trans. This
can advantageously be combined with -pbc mol -ur
compact.
-shift vector 0 0 0 All coordinates will be shifted by framenr*shift
-fit enum none Fit molecule to ref structure in the structure
file: none, rot+trans, rotxy+transxy,
translation, transxy or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool no Read and write forces if possible
-trunc time -1 Truncate input trajectory file after this time
(ps)
-exec string Execute command for every output frame with the
frame number as argument
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb
file
-nzero int 0 If the -sep flag is set, use these many digits
for the file numbers and prepend zeros as needed
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
-[no]conect bool no Add conect records when writing .pdb files.
Useful for visualization of non-standard
molecules, e.g. coarse grained ones
Will write pdb: Protein data bank file
Reading file ./sd.tpr, VERSION 4.5.5 (single precision)
Reading file ./sd.tpr, VERSION 4.5.5 (single precision)
Select group for output
Group 0 ( System) has 8 elements
Group 1 ( Other) has 8 elements
Group 2 ( ETH) has 8 elements
Select a group: Selected 0: 'System'
trn version: GMX_trn_file (single precision)
-> frame 250 time 250.000 -> frame 200 time 200.000
gcq#148: "Everybody's Good Enough For Some Change" (LIVE)
!tar cvf pdbs.tgz *.pdb
Визуализация¶
In [41]:
from IPython.display import Image
In [44]:
display(Image("../be.gif", format="png"))
In [45]:
display(Image("../an.gif", format="png"))
In [46]:
display(Image("../nh.gif", format="png"))
In [47]:
display(Image("../vr.gif", format="png"))
In [48]:
display(Image("../sd.gif", format="png"))
In [49]:
display(Image("../partyparrot.gif", format="png"))
Метод Андерсона практически заморозил молекулу, стохастическая МД температуру "снизить" достаточно не сумел. Берендсен показывает какое-то синхронное вращение обоих частей молекулы, это не так сильно похоже на тепловые колебания.
Графики¶
In [50]:
import numpy as np
import matplotlib.pyplot as plt
In [72]:
%%bash
echo "10 11\n\n" | g_energy -f be.edr -o be.xvg -xvg none
echo "10 11\n\n" | g_energy -f an.edr -o an.xvg -xvg none
echo "10 11\n\n" | g_energy -f vr.edr -o vr.xvg -xvg none
echo "10 11\n\n" | g_energy -f nh.edr -o nh.xvg -xvg none
echo "10 11\n\n" | g_energy -f sd.edr -o sd.xvg -xvg none
Statistics over 250001 steps [ 0.0000 through 250.0000 ps ], 2 data sets All statistics are over 25001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 26.2645 0.047 1.70731 0.289414 (kJ/mol) Kinetic En. 26.1643 0.026 1.71158 0.157078 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. Statistics over 250001 steps [ 0.0000 through 250.0000 ps ], 2 data sets All statistics are over 25001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 0.627746 0.00037 0.317314 0.00119048 (kJ/mol) Kinetic En. 0.758572 0.00039 0.305373 0.00155707 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. Statistics over 250001 steps [ 0.0000 through 250.0000 ps ], 2 data sets All statistics are over 25001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 26.1045 0.21 8.29619 0.151355 (kJ/mol) Kinetic En. 25.9961 0.21 7.89283 0.0764954 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. Statistics over 250001 steps [ 0.0000 through 250.0000 ps ], 2 data sets All statistics are over 25001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 8.77853 0.51 13.8869 -2.55711 (kJ/mol) Kinetic En. 25.9194 0.017 42.4831 -0.0685308 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. Statistics over 250001 steps [ 0.0000 through 250.0000 ps ], 2 data sets All statistics are over 25001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 22.6663 0.27 7.65454 1.679 (kJ/mol) Kinetic En. 26.6528 0.31 8.06 1.97782 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties.
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f be.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o be.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened be.edr as single precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Coulomb-(SR)
9 Coulomb-(LR) 10 Potential 11 Kinetic-En. 12 Total-Energy
13 Temperature 14 Pressure 15 Vir-XX 16 Vir-XY
17 Vir-XZ 18 Vir-YX 19 Vir-YY 20 Vir-YZ
21 Vir-ZX 22 Vir-ZY 23 Vir-ZZ 24 Pres-XX
25 Pres-XY 26 Pres-XZ 27 Pres-YX 28 Pres-YY
29 Pres-YZ 30 Pres-ZX 31 Pres-ZY 32 Pres-ZZ
33 #Surf*SurfTen 34 Mu-X 35 Mu-Y 36 Mu-Z
37 T-System 38 Lamb-System
Back Off! I just backed up be.xvg to ./#be.xvg.7#
Last energy frame read 2500 time 250.000
gcq#270: "AH ....Satisfaction" (IRIX imapd)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f an.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o an.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened an.edr as single precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Coulomb-(SR)
9 Coulomb-(LR) 10 Potential 11 Kinetic-En. 12 Total-Energy
13 Temperature 14 Pressure 15 Vir-XX 16 Vir-XY
17 Vir-XZ 18 Vir-YX 19 Vir-YY 20 Vir-YZ
21 Vir-ZX 22 Vir-ZY 23 Vir-ZZ 24 Pres-XX
25 Pres-XY 26 Pres-XZ 27 Pres-YX 28 Pres-YY
29 Pres-YZ 30 Pres-ZX 31 Pres-ZY 32 Pres-ZZ
33 #Surf*SurfTen 34 Mu-X 35 Mu-Y 36 Mu-Z
37 T-System
Last energy frame read 2500 time 250.000
gcq#270: "AH ....Satisfaction" (IRIX imapd)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f vr.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o vr.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened vr.edr as single precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Coulomb-(SR)
9 Coulomb-(LR) 10 Potential 11 Kinetic-En. 12 Total-Energy
13 Conserved-En. 14 Temperature 15 Pressure 16 Vir-XX
17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY
21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ
25 Pres-XX 26 Pres-XY 27 Pres-XZ 28 Pres-YX
29 Pres-YY 30 Pres-YZ 31 Pres-ZX 32 Pres-ZY
33 Pres-ZZ 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y
37 Mu-Z 38 T-System 39 Lamb-System
Last energy frame read 2500 time 250.000
gcq#270: "AH ....Satisfaction" (IRIX imapd)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f nh.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o nh.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened nh.edr as single precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Coulomb-(SR)
9 Coulomb-(LR) 10 Potential 11 Kinetic-En. 12 Total-Energy
13 Conserved-En. 14 Temperature 15 Pressure 16 Vir-XX
17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY
21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ
25 Pres-XX 26 Pres-XY 27 Pres-XZ 28 Pres-YX
29 Pres-YY 30 Pres-YZ 31 Pres-ZX 32 Pres-ZY
33 Pres-ZZ 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y
37 Mu-Z 38 T-System
Last energy frame read 2500 time 250.000
gcq#270: "AH ....Satisfaction" (IRIX imapd)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f sd.edr Input Energy file
-f2 ener.edr Input, Opt. Energy file
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o sd.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
-odh dhdl.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than display
them all
-[no]dp bool no Print energies in high precision
-nbmin int 5 Minimum number of blocks for error estimate
-nbmax int 5 Maximum number of blocks for error estimate
-[no]mutot bool no Compute the total dipole moment from the
components
-skip int 0 Skip number of frames between data points
-[no]aver bool no Also print the exact average and rmsd stored in
the energy frames (only when 1 term is requested)
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-[no]driftcorr bool no Useful only for calculations of fluctuation
properties. The drift in the observables will be
subtracted before computing the fluctuation
properties.
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Opened sd.edr as single precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Coulomb-(SR)
9 Coulomb-(LR) 10 Potential 11 Kinetic-En. 12 Total-Energy
13 Temperature 14 Pressure 15 Vir-XX 16 Vir-XY
17 Vir-XZ 18 Vir-YX 19 Vir-YY 20 Vir-YZ
21 Vir-ZX 22 Vir-ZY 23 Vir-ZZ 24 Pres-XX
25 Pres-XY 26 Pres-XZ 27 Pres-YX 28 Pres-YY
29 Pres-YZ 30 Pres-ZX 31 Pres-ZY 32 Pres-ZZ
33 #Surf*SurfTen 34 Mu-X 35 Mu-Y 36 Mu-Z
37 T-System
Last energy frame read 2500 time 250.000
gcq#270: "AH ....Satisfaction" (IRIX imapd)
In [79]:
def draw_plot(path, title):
mat = np.genfromtxt(path)
x, p, k = mat[:,0], mat[:,1], mat[:,2]
fig, ax = plt.subplots(figsize=(15,5))
ax.plot(x, p, label="Потенциальная энергия", color="orange")
ax.plot(x, k, label="Кинетическая энергия", color="blue")
ax.set_title(f"Метод {title}", fontdict={"fontsize" : 16})
ax.set_xlabel("время (пс)", fontdict={"fontsize" : 12})
ax.set_ylabel("энергия, кДж/моль", fontdict={"fontsize" : 12})
ax.legend()
def draw_hist(path, title):
mat = np.genfromtxt(path)
x, y = mat[:,0], mat[:,1]
fig, ax = plt.subplots(figsize=(8,4))
ax.bar(x, y, width = 0.0002, color="cadetblue")
ax.set_title("Метод {}".format(title), fontdict={"fontsize" : 18})
ax.set_xlabel("длина связи (нм)", fontdict={"fontsize" : 14})
In [73]:
draw_plot("be.xvg", "Берендсена")
Метод сходится к одному состоянию, при этом не минимальной энергии
In [74]:
draw_plot("vr.xvg", "'Velocity Rescale'")
Значительные колебания вокруг постоянных значений энергии
In [75]:
draw_plot("nh.xvg", "Нуза-Хувера")
Очень большие выбросы по энергии
In [76]:
draw_plot("an.xvg", "Андерсена")
Система почти заморожена
In [77]:
draw_plot("sd.xvg", "стохастической МД")
Большой разброс, похож на VR
Распределение длины связей¶
In [84]:
%%bash
echo "[ b ]" > b.ndx
echo "1 2" >> b.ndx
In [89]:
%%bash
g_bond -f be.trr -s be.tpr -o bond_be.xvg -n b.ndx -xvg none
g_bond -f an.trr -s an.tpr -o bond_an.xvg -n b.ndx -xvg none
g_bond -f nh.trr -s nh.tpr -o bond_nh.xvg -n b.ndx -xvg none
g_bond -f vr.trr -s vr.tpr -o bond_vr.xvg -n b.ndx -xvg none
g_bond -f sd.trr -s sd.tpr -o bond_sd.xvg -n b.ndx -xvg none
Total number of samples : 251 Mean : 0.153135 Standard deviation of the distribution: 0.00177711 Standard deviation of the mean : 0.00011217 Total number of samples : 251 Mean : 0.153024 Standard deviation of the distribution: 0.00143875 Standard deviation of the mean : 9.08129e-05 Total number of samples : 251 Mean : 0.153033 Standard deviation of the distribution: 0.00293297 Standard deviation of the mean : 0.000185128 Total number of samples : 251 Mean : 0.153297 Standard deviation of the distribution: 0.00371384 Standard deviation of the mean : 0.000234415 Total number of samples : 251 Mean : 0.153194 Standard deviation of the distribution: 0.00337451 Standard deviation of the mean : 0.000212997
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f be.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s be.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_be.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.1#
Reading frame 200 time 200.000
Back Off! I just backed up bond_be.xvg to ./#bond_be.xvg.1#
gcq#191: "How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control)
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f an.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s an.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_an.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.2#
Reading frame 200 time 200.000
gcq#191: "How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control)
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f nh.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s nh.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_nh.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.3#
Reading frame 200 time 200.000
gcq#191: "How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control)
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f vr.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s vr.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_vr.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.4#
Reading frame 200 time 200.000
gcq#191: "How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control)
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_bond (-:
Option Filename Type Description
------------------------------------------------------------
-f sd.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n b.ndx Input Index file
-s sd.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-o bond_sd.xvg Output xvgr/xmgr file
-l bonds.log Output, Opt. Log file
-d distance.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum none xvg plot formatting: xmgrace, xmgr or none
-blen real -1 Bond length. By default length of first bond
-tol real 0.1 Half width of distribution as fraction of -blen
-[no]aver bool yes Average bond length distributions
-[no]averdist bool yes Average distances (turns on -d)
Group 0 ( b) has 2 elements
There is one group in the index
Will gather information on 1 bonds
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up distance.xvg to ./#distance.xvg.5#
Reading frame 200 time 200.000
gcq#191: "How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control)
In [90]:
draw_hist("bond_be.xvg", "Берендсена")
In [92]:
draw_hist("bond_an.xvg", "Андерсона")
Странные пики по краям распределения
In [93]:
draw_hist("bond_nh.xvg", "Нуза-Хувера")
In [94]:
draw_hist("bond_vr.xvg", "Velociry rescale")
In [95]:
draw_hist("bond_sd.xvg", "стохастической МД")
Некоторые недостатки методов были перечислены в ходе работы. Наиболее странный вид имеет метод Андерсона, распределение энергий в нем узкое и имеет тяжелые пики. Кажется, лучше всего показал себя метод VR, он адекватно контроллировал температуру, показывал колебания, похожие на тепловые, имеет правдоподобные распределения.
Зависимость времени выполнения от алгоритма (мс)¶
In [96]:
import pandas as pd
dat = [5743, 5627, 5551, 4872, 5571]
pd.DataFrame(dat).rename(
{0 : 'an', 1 : 'be', 2 : 'vr', 3 : 'sd', 4 : 'nh'}
).T
Out[96]:
| an | be | vr | sd | nh | |
|---|---|---|---|---|---|
| 0 | 5743 | 5627 | 5551 | 4872 | 5571 |