In [1]:
%%bash
export PATH=${PATH}:/home/preps/golovin/progs/bin
export MOPAC_LICENSE=/home/preps/golovin/progs/bin
obgen nap.smi > nap.mol
obgen azul.smi > azul.mol

A T O M   T Y P E S

IDX	TYPE
1	37
2	37
3	37
4	37
5	37
6	37
7	37
8	37
9	37
10	37
11	5
12	5
13	5
14	5
15	5
16	5
17	5
18	5

F O R M A L   C H A R G E S

IDX	CHARGE
1	0.000000
2	0.000000
3	0.000000
4	0.000000
5	0.000000
6	0.000000
7	0.000000
8	0.000000
9	0.000000
10	0.000000
11	0.000000
12	0.000000
13	0.000000
14	0.000000
15	0.000000
16	0.000000
17	0.000000
18	0.000000

P A R T I A L   C H A R G E S

IDX	CHARGE
1	-0.150000
2	-0.150000
3	-0.150000
4	0.000000
5	-0.150000
6	-0.150000
7	-0.150000
8	-0.150000
9	0.000000
10	-0.150000
11	0.150000
12	0.150000
13	0.150000
14	0.150000
15	0.150000
16	0.150000
17	0.150000
18	0.150000

S E T T I N G   U P   C A L C U L A T I O N S

SETTING UP BOND CALCULATIONS...
SETTING UP ANGLE & STRETCH-BEND CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
SETTING UP ELECTROSTATIC CALCULATIONS...

S T E E P E S T   D E S C E N T

STEPS = 500

STEP n       E(n)         E(n-1)    
------------------------------------
    0      78.012      ----
   10    43.02518    44.38509
   20    35.15990    35.46349
   30    33.18804    33.34898
   40    32.10727    32.29781
   50    31.69157    31.70113
   60    31.53407    31.54209
   70    31.46249    31.46901
   80    31.40430    31.40953
   90    31.35732    31.36175
  100    31.31755    31.32116
  110    31.28505    31.28801
  120    31.25841    31.26084
  130    31.23652    31.23852
  140    31.21135    31.21578
  150    31.19748    31.19874
  160    31.18460    31.18636
  170    31.16975    31.17050
  180    31.16203    31.16285
  190    31.15462    31.15676
  200    31.14928    31.15083
  210    31.14598    31.14618
  220    31.14308    31.14327
    STEEPEST DESCENT HAS CONVERGED

W E I G H T E D   R O T O R   S E A R C H

  NUMBER OF ROTATABLE BONDS: 0
  NUMBER OF POSSIBLE ROTAMERS: 1
  GENERATED ONLY ONE CONFORMER


S T E E P E S T   D E S C E N T

STEPS = 500

STEP n       E(n)         E(n-1)    
------------------------------------
    0      31.135      ----
   10    31.13334    31.13409
   20    31.13312    31.13340
   30    31.13302    31.13314
   40    31.13385    31.13302
   50    31.13334    31.13296
   60    31.13310    31.13353
   70    31.13298    31.13319
   80    31.13292    31.13302
   90    31.13361    31.13294
  100    31.13323    31.13397
  110    31.13304    31.13340
  120    31.13294    31.13312
  130    31.13290    31.13299
  140    31.13355    31.13292
  150    31.13321    31.13392
  160    31.13303    31.13339
  170    31.13294    31.13313
  180    31.13289    31.13299
  190    31.13362    31.13292
  200    31.13326    31.13288
  210    31.13306    31.13349
  220    31.13296    31.13319
  230    31.13290    31.13303
  240    31.13382    31.13294
  250    31.13338    31.13290
  260    31.13313    31.13368
  270    31.13300    31.13330
  280    31.13293    31.13310
  290    31.13289    31.13298
  300    31.13358    31.13292
  310    31.13325    31.13288
  320    31.13307    31.13349
  330    31.13297    31.13321
  340    31.13291    31.13304
  350    31.13391    31.13295
  360    31.13344    31.13290
  370    31.13318    31.13379
  380    31.13303    31.13338
  390    31.13295    31.13314
  400    31.13290    31.13301
  410    31.13373    31.13293
  420    31.13334    31.13289
  430    31.13312    31.13364
  440    31.13300    31.13329
  450    31.13293    31.13310
  460    31.13289    31.13298
  470    31.13360    31.13292
  480    31.13327    31.13288
  490    31.13308    31.13352
  500    31.13298    31.13323

A T O M   T Y P E S

IDX	TYPE
1	2
2	2
3	2
4	2
5	2
6	2
7	2
8	2
9	2
10	2
11	5
12	5
13	5
14	5
15	5
16	5
17	5
18	5

F O R M A L   C H A R G E S

IDX	CHARGE
1	0.000000
2	0.000000
3	0.000000
4	0.000000
5	0.000000
6	0.000000
7	0.000000
8	0.000000
9	0.000000
10	0.000000
11	0.000000
12	0.000000
13	0.000000
14	0.000000
15	0.000000
16	0.000000
17	0.000000
18	0.000000

P A R T I A L   C H A R G E S

IDX	CHARGE
1	-0.150000
2	-0.150000
3	-0.150000
4	0.000000
5	-0.150000
6	-0.150000
7	-0.150000
8	0.000000
9	-0.150000
10	-0.150000
11	0.150000
12	0.150000
13	0.150000
14	0.150000
15	0.150000
16	0.150000
17	0.150000
18	0.150000

S E T T I N G   U P   C A L C U L A T I O N S

SETTING UP BOND CALCULATIONS...
SETTING UP ANGLE & STRETCH-BEND CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
SETTING UP ELECTROSTATIC CALCULATIONS...

S T E E P E S T   D E S C E N T

STEPS = 500

STEP n       E(n)         E(n-1)    
------------------------------------
    0    100516.997      ----
   10    638.25949    708.06367
   20    212.89903    224.20906
   30    151.64448    155.87394
   40    123.24070    125.56103
   50    104.95487    105.67845
   60    94.14826    94.63131
   70    88.60429    88.85189
   80    86.25816    86.34151
   90    85.07646    85.12835
  100    84.40289    84.44227
  110    83.92500    83.96032
  120    83.55584    83.58161
  130    83.25644    83.27731
  140    83.00713    83.02518
  150    82.79644    82.81290
  160    82.61825    82.63271
  170    82.46517    82.47477
  180    82.33435    82.34415
  190    82.22332    82.23239
  200    82.13605    82.13866
  210    82.05573    82.05825
  220    82.00641    82.00950
  230    81.96111    81.96407
  240    81.92770    81.92840
  250    81.89619    81.89843
  260    81.86228    81.86447
  270    81.83806    81.83781
  280    81.78124    81.78216
  290    81.74541    81.74863
  300    81.72741    81.72839
  310    81.70244    81.70470
  320    81.68156    81.68351
  330    81.66924    81.66962
  340    81.66064    81.66238
  350    81.64784    81.64832
  360    81.64053    81.64080
  370    81.63010    81.63429
  380    81.62454    81.62531
  390    81.62129    81.62157
  400    81.61693    81.61717
  410    81.61190    81.61326
  420    81.60848    81.60861
  430    81.60517    81.60532
  440    81.60258    81.60389
  450    81.60012    81.60045
    STEEPEST DESCENT HAS CONVERGED

W E I G H T E D   R O T O R   S E A R C H

  NUMBER OF ROTATABLE BONDS: 0
  NUMBER OF POSSIBLE ROTAMERS: 1
  GENERATED ONLY ONE CONFORMER


S T E E P E S T   D E S C E N T

STEPS = 500

STEP n       E(n)         E(n-1)    
------------------------------------
    0      81.586      ----
   10    81.58479    81.58493
   20    81.58479    81.58445
   30    81.58418    81.58477
   40    81.58354    81.58382
   50    81.58319    81.58337
   60    81.58380    81.58287
   70    81.58292    81.58259
   80    81.58253    81.58304
   90    81.58209    81.58234
  100    81.58188    81.58204
  110    81.58258    81.58169
  120    81.58186    81.58152
  130    81.58157    81.58206
  140    81.58124    81.58148
  150    81.58111    81.58126
  160    81.58189    81.58099
  170    81.58124    81.58089
  180    81.58102    81.58151
  190    81.58074    81.58098
  200    81.58066    81.58082
  210    81.58151    81.58058
  220    81.58090    81.58052
  230    81.58071    81.58122
  240    81.58045    81.58071
  250    81.58040    81.58056
  260    81.58027    81.58035
  270    81.58073    81.58030
  280    81.58055    81.58110
  290    81.58029    81.58057
  300    81.58025    81.58044
  310    81.58013    81.58022
  320    81.58067    81.58019
  330    81.58048    81.58111
  340    81.58022    81.58054
  350    81.58017    81.58039
  360    81.58006    81.58016
  370    81.58071    81.58013
  380    81.58049    81.58002
  390    81.58019    81.58058
  400    81.58015    81.58040
  410    81.58002    81.58014
  420    81.58085    81.58011
  430    81.58056    81.58000
  440    81.58022    81.58071
  450    81.58015    81.58047
  460    81.58001    81.58017
  470    81.58110    81.58012
  480    81.58071    81.57999
  490    81.58029    81.58094
  500    81.58019    81.58061
In [5]:
import __main__
In [6]:
__main__.pymol_argv = [ 'pymol', '-cp' ]

### Если вывод в графическое окно тормозит или не нужен, то:
##__main__.pymol_argv = [ 'pymol', '-cp' ]


import pymol
 
pymol.finish_launching()
 
from pymol import cmd
cmd.load("azul.mol")
cmd.save("azul.pdb")
In [9]:
cmd.load("nap.mol")
cmd.save("nap.pdb","nap")
In [27]:
%%bash
babel -ipdb azul.pdb -omop azul_opt.mop -xk "PM6"
In [28]:
%%bash
export PATH=${PATH}:/home/preps/golovin/progs/bin
export MOPAC_LICENSE=/home/preps/golovin/progs/bin
MOPAC2009.exe azul_opt.mop
In [30]:
%%bash
babel -imopout azul_opt.out -opdb azul_opt.pdb
In [32]:
%%bash
obgen azul.smi -ff MMFF94 > azul2.mol
In [33]:
cmd.load("azul2.mol")
cmd.save("azul2.pdb","azul2")
In [34]:
%%bash
babel -ipdb azul2.pdb -omop azul2_opt.mop -xk "PM6"
export PATH=${PATH}:/home/preps/golovin/progs/bin
export MOPAC_LICENSE=/home/preps/golovin/progs/bin
MOPAC2009.exe azul2_opt.mop
In [36]:
%%bash
babel -imopout azul2_opt.out -opdb azul2_opt.pdb
In [37]:
%%bash
babel -ipdb nap.pdb -omop nap_opt.mop -xk "PM6"
export PATH=${PATH}:/home/preps/golovin/progs/bin
export MOPAC_LICENSE=/home/preps/golovin/progs/bin
MOPAC2009.exe nap_opt.mop
In [38]:
%%bash
babel -imopout nap_opt.out -opdb nap_opt.pdb
In [54]:
%%bash
babel -ipdb azul2_opt.pdb -ogamin azul.gamin
babel -ipdb nap_opt.pdb -ogamin nap.gamin
In [55]:
%%bash
HEADER=" \$CONTRL COORD=CART UNITS=ANGS   SCFTYP=RHF RUNTYP=OPTIMIZE \$END\n\
 \$BASIS  GBASIS=N31 NGAUSS=6  \$end\n\
 \$system mwords=2 \$end\n\
 \$DATA"

echo -en " " > azul2_opt.inp
echo -e $HEADER >> azul2_opt.inp
tail -n+4 azul.gamin >> azul2_opt.inp

echo -en " " >> nap_opt.inp
echo -e $HEADER > nap_opt.inp
tail -n+4 nap.gamin >> nap_opt.inp
In [56]:
%%bash
gms nap_opt.inp 1 | tee nap_opt.log 
gms azul2_opt.inp 1 | tee azul_opt.log
In [57]:
%%bash
babel -igamout azul_opt.log -ogamin azul_gamout.inp
babel -igamout nap_opt.log -ogamin nap_gamout.inp

HF_HEADER="\$CONTRL COORD=CART UNITS=ANGS   SCFTYP=RHF RUNTYP=ENERGY \$END\n\
 \$BASIS  GBASIS=N31 NGAUSS=6\n\
  POLAR=POPN31 NDFUNC=1 \$END\n\
 \$GUESS  GUESS=HUCKEL \$END\n\
 \$system mwords=2 \$end\n\
 \$DATA"

echo -en " " > azul_hart.inp
echo -e $HF_HEADER >> azul_hart.inp
tail -n+4 azul_gamout.inp >> azul_hart.inp

echo -en " " > nap_hart.inp
echo -e $HF_HEADER >> nap_hart.inp
tail -n+4 nap_gamout.inp >> nap_hart.inp
In [58]:
%%bash
gms nap_hart.inp  1 >& nap_hart.log 
gms azul_hart.inp  1 >& azul_hart.log
In [60]:
%%bash
grep "TOTAL ENERGY =" azul_hart.log nap_hart.log
По Хартри-Фоку получилось 45.6 кКал/моль, а по теории функционала плотности - 34.3, это ближе к экспериментальному значению (35.3±2.2). Таким образом, метод DFT является более точным.
In [ ]: