import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem, Draw
from rdkit.Chem import Descriptors
from rdkit import RDConfig
from IPython.display import Image,display
import numpy as np
import os
! wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro
! mv etane.gro ethane.gro
--2019-05-20 02:30:27-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro Resolving kodomo.fbb.msu.ru... 192.168.180.1 Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 399 Saving to: `etane.gro' 100%[======================================>] 399 --.-K/s in 0s 2019-05-20 02:30:27 (44.3 MB/s) - `etane.gro' saved [399/399]
%%bash
cat /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
; 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.
# создадим этан
mol=Chem.MolFromSmiles('CC')
AllChem.Compute2DCoords(mol)
m3d=Chem.AddHs(mol)
Chem.AllChem.EmbedMolecule(m3d)
AllChem.MMFFOptimizeMolecule(m3d,maxIters=500,nonBondedThresh=200 )
0
# и придумаем циклы
## связи
bonds = m3d.GetBonds()
for i,b in enumerate(bonds):
print (b.GetBeginAtomIdx() , b.GetEndAtomIdx())
0 1 0 2 0 3 0 4 1 5 1 6 1 7
## углы
for b1 in m3d.GetBonds():
for b2 in m3d.GetBonds():
if b1.GetBeginAtomIdx() == b2.GetBeginAtomIdx() and b1.GetIdx() != b2.GetIdx():
print (b1.GetEndAtomIdx() + 1, b1.GetBeginAtomIdx() + 1, b2.GetEndAtomIdx() + 1, '1')
2 1 3 1 2 1 4 1 2 1 5 1 3 1 2 1 3 1 4 1 3 1 5 1 4 1 2 1 4 1 3 1 4 1 5 1 5 1 2 1 5 1 3 1 5 1 4 1 6 2 7 1 6 2 8 1 7 2 6 1 7 2 8 1 8 2 6 1 8 2 7 1
#торсионные углы
for b1 in m3d.GetBonds():
for b2 in m3d.GetBonds():
for b3 in m3d.GetBonds():
if b1.GetBeginAtomIdx() == b2.GetBeginAtomIdx() and b1.GetIdx() != b2.GetIdx() and b2.GetEndAtomIdx()==b3.GetBeginAtomIdx() and b3.GetIdx() != b2.GetIdx():
print (b1.GetEndAtomIdx()+1, b1.GetBeginAtomIdx()+1, b2.GetEndAtomIdx()+1, b3.GetEndAtomIdx()+1, '3')
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
Нужные строки из atomtypes.atp: opls_139 12.01100 ; alkane C opls_140 1.00800 ; alkane H.
Соберем файл et.top
%%bash
echo '#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_139 1 ETH C1 1 -0.189 12.01
2 opls_139 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
6 2 8 1
6 2 7 1
7 2 8 1
1 2 7 1
1 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
[ System ]
; any text here
first one
[ molecules ]
;Name count
et 1' > et.top
%%bash
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_139 1 ETH C1 1 -0.189 12.01
2 opls_139 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
6 2 8 1
6 2 7 1
7 2 8 1
1 2 7 1
1 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
[ System ]
; any text here
first one
[ molecules ]
;Name count
et 1
скачаем 5 конфигурационных файлов
for i in ['be', 'vr', 'nh', 'an', 'sd']:
# скачаем конфгурацонный файл
os.system('wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/%s.mdp' % i)
# построим входные файлы для молекулярно-динамического движка
os.system('grompp -f %s.mdp -c etane.gro -p ethane.top -o ethane_%s.tpr' % (i,i))
# запустим mdrun
os.system('mdrun -deffnm ethane_%s -v -nt 1' % i)
# проведем конвертацию в pdb
os.system('echo 0 | trjconv -f ethane_%s.trr -s ethane_%s.tpr -o ethane_%s.pdb' % (i,i,i))
# Сравним потенциальную энергию и кинетическую энергию для каждой из 5 систем
os.system('echo 10 | g_energy -f ethane_%s.edr -o ethane_%s_pot.xvg -xvg none' % (i,i))
os.system('echo 11 | g_energy -f ethane_%s.edr -o ethane_%s_kin.xvg -xvg none' % (i,i))
#запустим утилиту по анализу связей g_bond:
os.system('g_bond -f ethane_%s.trr -s ethane_%s.tpr -o bond_%s.xvg -n b.ndx -xvg none' % (i,i,i))
print ('%s ok' % i)
be ok vr ok nh ok an ok sd ok
нужно построить графики изменения кинетической и потенциальной энергий
import numpy as np
import matplotlib.pyplot as plt
list1 = ['be', 'vr', 'nh', 'an', 'sd']
for i in list1:
a = np.loadtxt('ethane_%s_pot.xvg' % i)
b = np.loadtxt('ethane_%s_kin.xvg' % i)
x_1=a[:,0]
y_1=a[:,1]
x_2=b[:,0]
y_2=b[:,1]
plt.plot(x_1,y_1,"b-",alpha=0.3,label="Potential Energy")
plt.plot(x_2,y_2,"r-",alpha=0.3,label="Kinetic Energy")
plt.title(prog_list[i]+": potential vs kinetic energy")
plt.ylabel('Energy, kJ/mol')
plt.xlabel('Time, ps')
--------------------------------------------------------------------------- OSError Traceback (most recent call last) <ipython-input-43-51ff187e2cf8> in <module> 3 list1 = ['be', 'vr', 'nh', 'an', 'sd'] 4 for i in list1: ----> 5 a = np.loadtxt('ethane_%s_pot.xvg' % i) 6 b = np.loadtxt('ethane_%s_kin.xvg' % i) 7 x_1=a[:,0] /home/preps/golovin/miniconda2/envs/molsim/lib/python3.7/site-packages/numpy/lib/npyio.py in loadtxt(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin, encoding, max_rows) 953 fname = os_fspath(fname) 954 if _is_string_like(fname): --> 955 fh = np.lib._datasource.open(fname, 'rt', encoding=encoding) 956 fencoding = getattr(fh, 'encoding', 'latin1') 957 fh = iter(fh) /home/preps/golovin/miniconda2/envs/molsim/lib/python3.7/site-packages/numpy/lib/_datasource.py in open(path, mode, destpath, encoding, newline) 264 265 ds = DataSource(destpath) --> 266 return ds.open(path, mode, encoding=encoding, newline=newline) 267 268 /home/preps/golovin/miniconda2/envs/molsim/lib/python3.7/site-packages/numpy/lib/_datasource.py in open(self, path, mode, encoding, newline) 622 encoding=encoding, newline=newline) 623 else: --> 624 raise IOError("%s not found." % path) 625 626 OSError: ethane_be_pot.xvg not found.
grompp на kodomo не работает сейчас корректно, так как не делается .tpr-файл. дальше работать не получится...