Computing CHARMM FF energy using GMIN, MMTSB and CHARMM
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Below script (compare.sh) computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB options.
ss2029@clust:~/WORK/compareCharmmEnergies> ls compare.sh /home/ss2029/svn/GMIN/bin/CGMIN35.serial gmin.log echo ============GMIN=========================== grep '1 energy' gmin.log echo ============MMTSB========================== enerCHARMM.pl -psf input.psf input.crd -par gb=0,cutnb=999,cuton=979,cutoff=989,param=27 -out total dbase.1.pdb echo ============CHARMM========================= ~/svn/CHARMM35/exec/gnu/charmm < ener.inp > charmm.log grep 'ENER>' charmm.log
The required input files (GMIN data file, Charmm script, Charmm psf and Charmm crd) are listed below. The psf and crd files are for dialanine.
GMIN data file
MAXERISE 1.0D-1 ACCEPTRATIO 0.3 comment CENTRE EDIFF 0.05 UPDATES 100 TEMPERATURE 1.0 comment MAXIT 0 0 - no quenching MAXIT 0 0 comment STEPS 0 1.0 - no hopping STEPS 0 1.0 STEP 0.03 0.0 SAVE 50 CHARMMTYPE toph19_eef1_perm.in param19_eef1_perm.in CHARMM * PRNLEV 0 BOMLev -2 set pardir "/home/ss2029/svn/CHARMM35/toppar" ! READ TOPOLOGY open unit 1 read formatted name @pardir/"top_all27_prot_na.rtf" read rtf card unit 1 close unit 1 ! READ PARAMS open unit 2 read formatted name @pardir/"par_all27_prot_na.prm" read para card unit 2 close unit 2 ! read psf open unit 1 form read name input.psf read psf card unit 1 close unit 1 ! read crd open unit 20 name input.crd read card READ COOR UNIT 20 CARD FREE CLOSE UNIT 20 UPDATE NBOND atom switch cdie vdw vswitch - ctonnb 979 ctofnb 989 cutnb 999 PRNLEV 0 WRNLEV 0
Charmm script
bomblev -2 ! SET PATH to topology and parameter files ! quotes MUST if path has both upper and lower case letters set pardir "/home/ss2029/svn/CHARMM35/toppar" ! READ TOPOLOGY open unit 1 read formatted name @pardir/"top_all27_prot_na.rtf" read rtf card unit 1 close unit 1 ! READ PARAMS open unit 2 read formatted name @pardir/"par_all27_prot_na.prm" read para card unit 2 close unit 2 ! READ psf from file open unit 1 form read name input.psf read psf card unit 1 close unit 1 ! ! Energies are sensible only if coordinates are read from crd, not pdb ! ! READ coord from crd !open unit 1 card read name dbase.1 open unit 1 card read name input.crd read coor card unit 1 close unit 1 ! set ff parameters UPDATE NBOND atom switch cdie vdw vswitch - ctonnb 979 ctofnb 989 cutnb 999 ! energy before min ENERgy STOP
Charmm crd
* NONE *
* DATE: 8/10/11 5:30:23 CREATED BY USER: ss2029
*
32 EXT
1 1 ALA CAY -2.1597208496 0.5369209221 0.9299743167 DIALA 1 0.0000000000
2 1 ALA HY1 -2.4659539520 0.0029400500 0.0050923160 DIALA 1 0.0000000000
3 1 ALA HY2 -2.5618558380 1.5723870611 0.9095212950 DIALA 1 0.0000000000
4 1 ALA HY3 -2.5618558380 0.0014750162 1.8164877870 DIALA 1 0.0000000000
5 1 ALA CY -0.6725000000 0.5824020840 1.0087500000 DIALA 1 0.0000000000
6 1 ALA OY -0.1045492057 1.1279137464 1.9536039154 DIALA 1 0.0000000000
7 1 ALA N 0.0000000000 0.0000000000 0.0000000000 DIALA 1 0.0000000000
8 1 ALA HN -0.4526285282 -0.4441667523 -0.7693193820 DIALA 1 0.0000000000
9 1 ALA CA 1.4592000000 0.0000000000 0.0000000000 DIALA 1 0.0000000000
10 1 ALA HA 1.8124541037 -0.4965229490 0.8965112935 DIALA 1 0.0000000000
11 1 ALA CB 1.9486982186 -0.8335550140 -1.2066493868 DIALA 1 0.0000000000
12 1 ALA HB1 1.5137367553 -1.8544732629 -1.1553340411 DIALA 1 0.0000000000
13 1 ALA HB2 1.6279547656 -0.3731122917 -2.1665648762 DIALA 1 0.0000000000
14 1 ALA HB3 3.0556965246 -0.9321006383 -1.2139617347 DIALA 1 0.0000000000
15 1 ALA C 2.0959460235 1.4010979629 0.0000000000 DIALA 1 0.0000000000
16 1 ALA O 1.4254835730 2.4319433404 0.0000000000 DIALA 1 0.0000000000
17 2 ALA N 3.4505567565 1.4578729742 0.0000000000 DIALA 2 0.0000000000
18 2 ALA HN 3.9535262716 0.5940316537 0.0000000000 DIALA 2 0.0000000000
19 2 ALA CA 4.2755116024 2.6640434399 0.0000000000 DIALA 2 0.0000000000
20 2 ALA HA 4.0651012609 3.2359271596 -0.8965112935 DIALA 2 0.0000000000
21 2 ALA CB 3.8638264508 3.5386506679 1.2066493868 DIALA 2 0.0000000000
22 2 ALA HB1 2.7756002095 3.7559734531 1.1553340411 DIALA 2 0.0000000000
23 2 ALA HB2 4.0628092381 3.0139700855 2.1665648762 DIALA 2 0.0000000000
24 2 ALA HB3 4.4074251611 4.5080096993 1.2139617347 DIALA 2 0.0000000000
25 2 ALA C 5.7914561039 2.3986507715 0.0000000000 DIALA 2 0.0000000000
26 2 ALA O 6.5972739840 3.3279287408 0.0000000000 DIALA 2 0.0000000000
27 2 ALA NT 6.1750320160 1.1095058923 0.0000000000 DIALA 2 0.0000000000
28 2 ALA HNT 5.5284590189 0.3505906405 0.0000000000 DIALA 2 0.0000000000
29 2 ALA CAT 7.5659278107 0.7773780735 0.0000000000 DIALA 2 0.0000000000
30 2 ALA HT1 8.0482644114 1.2005614688 0.9069664920 DIALA 2 0.0000000000
31 2 ALA HT2 7.6834087533 -0.3273930468 0.0000000000 DIALA 2 0.0000000000
32 2 ALA HT3 8.0482644114 1.2005614688 -0.9069664920 DIALA 2 0.0000000000
Charmm psf
PSF EXT CMAP CHEQ
2 !NTITLE
* NONE *
* DATE: 8/10/11 5:30:23 CREATED BY USER: ss2029
32 !NATOM
1 DIALA 1 ALA CAY 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
2 DIALA 1 ALA HY1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
3 DIALA 1 ALA HY2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
4 DIALA 1 ALA HY3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
5 DIALA 1 ALA CY 20 0.510000 12.0110 0 0.00000 -0.301140E-02
6 DIALA 1 ALA OY 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
7 DIALA 1 ALA N 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
8 DIALA 1 ALA HN 1 0.310000 1.00800 0 0.00000 -0.301140E-02
9 DIALA 1 ALA CA 22 0.700000E-01 12.0110 0 0.00000 -0.301140E-02
10 DIALA 1 ALA HA 6 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
11 DIALA 1 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
12 DIALA 1 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
13 DIALA 1 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
14 DIALA 1 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
15 DIALA 1 ALA C 20 0.510000 12.0110 0 0.00000 -0.301140E-02
16 DIALA 1 ALA O 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
17 DIALA 2 ALA N 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
18 DIALA 2 ALA HN 1 0.310000 1.00800 0 0.00000 -0.301140E-02
19 DIALA 2 ALA CA 22 0.700000E-01 12.0110 0 0.00000 -0.301140E-02
20 DIALA 2 ALA HA 6 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
21 DIALA 2 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
22 DIALA 2 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
23 DIALA 2 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
24 DIALA 2 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
25 DIALA 2 ALA C 20 0.510000 12.0110 0 0.00000 -0.301140E-02
26 DIALA 2 ALA O 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
27 DIALA 2 ALA NT 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
28 DIALA 2 ALA HNT 1 0.310000 1.00800 0 0.00000 -0.301140E-02
29 DIALA 2 ALA CAT 24 -0.110000 12.0110 0 0.00000 -0.301140E-02
30 DIALA 2 ALA HT1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
31 DIALA 2 ALA HT2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
32 DIALA 2 ALA HT3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
31 !NBOND: bonds
5 1 5 7 1 2 1 3
1 4 6 5 11 9 7 8
7 9 15 9 15 17 9 10
11 12 11 13 11 14 16 15
21 19 17 18 17 19 25 19
19 20 21 22 21 23 21 24
26 25 25 27 27 28 27 29
29 30 29 31 29 32
54 !NTHETA: angles
2 1 3 2 1 4 2 1 5
3 1 4 3 1 5 4 1 5
1 5 6 1 5 7 6 5 7
5 7 8 5 7 9 8 7 9
7 9 10 7 9 11 7 9 15
10 9 11 10 9 15 11 9 15
9 11 12 9 11 13 9 11 14
12 11 13 12 11 14 13 11 14
9 15 16 9 15 17 16 15 17
15 17 18 15 17 19 18 17 19
17 19 20 17 19 21 17 19 25
20 19 21 20 19 25 21 19 25
19 21 22 19 21 23 19 21 24
22 21 23 22 21 24 23 21 24
19 25 26 19 25 27 26 25 27
25 27 28 25 27 29 28 27 29
27 29 30 27 29 31 27 29 32
30 29 31 30 29 32 31 29 32
66 !NPHI: dihedrals
1 5 7 8 1 5 7 9
2 1 5 6 2 1 5 7
3 1 5 6 3 1 5 7
4 1 5 6 4 1 5 7
5 7 9 10 5 7 9 11
5 7 9 15 6 5 7 8
6 5 7 9 7 9 11 12
7 9 11 13 7 9 11 14
7 9 15 16 7 9 15 17
8 7 9 10 8 7 9 11
8 7 9 15 9 15 17 18
9 15 17 19 10 9 11 12
10 9 11 13 10 9 11 14
10 9 15 16 10 9 15 17
11 9 15 16 11 9 15 17
12 11 9 15 13 11 9 15
14 11 9 15 15 17 19 20
15 17 19 21 15 17 19 25
16 15 17 18 16 15 17 19
17 19 21 22 17 19 21 23
17 19 21 24 17 19 25 26
17 19 25 27 18 17 19 20
18 17 19 21 18 17 19 25
19 25 27 28 19 25 27 29
20 19 21 22 20 19 21 23
20 19 21 24 20 19 25 26
20 19 25 27 21 19 25 26
21 19 25 27 22 21 19 25
23 21 19 25 24 21 19 25
25 27 29 30 25 27 29 31
25 27 29 32 26 25 27 28
26 25 27 29 28 27 29 30
28 27 29 31 28 27 29 32
6 !NIMPHI: impropers
5 1 7 6 7 5 9 8
15 9 17 16 17 15 19 18
27 25 29 28 25 19 27 26
3 !NDON: donors
7 8 17 18 27 28
3 !NACC: acceptors
6 5 16 15 26 25
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
9 0 !NGRP NST2
0 1 0 4 1 0 6 1 0
10 1 0 14 1 0 16 1 0
20 1 0 24 1 0 26 1 0
1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
0 0 !NUMLP NUMLPH
2 !NCRTERM: cross-terms
5 7 9 15 7 9 15 17
15 17 19 25 17 19 25 27
--Ss2029 15:48, 7 September 2011 (UTC)