Yes. We got a lig.prm
file and it was #included
in the topol.top
file. Despite this, the above mention error was occurred.
The ligand we employed was Pixantrone. We drew this structure, minimized it and then docked it in out target protein.
An analog of this ligand can be found in the pdb 4G0W.
I am unable to upload the ligand files. It says that new users can not upload documents and I joined this forum today itself! Hence, I shall paste the content of those files here itself.
LIG.mol2
@<TRIPOS>MOLECULE
LIG
43 45 1
SMALL
USER_CHARGES
****
gtpase kras; chain: a; synonym: k-ras 2,ki-ras,c-k-ras,c-ki-ras; engineered: yes
@<TRIPOS>ATOM
1 H91 7.7930 -3.1192 62.9906 H 1 LIG1 0.1500
2 C9 7.8087 -4.0433 62.4242 C.ar 1 LIG1 -0.1500
3 C10 6.6293 -4.7505 62.3423 C.ar 1 LIG1 -0.1500
4 H101 5.7678 -4.3354 62.8521 H 1 LIG1 0.1500
5 C7 6.5338 -5.9411 61.6386 C.ar 1 LIG1 0.1000
6 N2 5.3010 -6.6409 61.5592 N.pl3 1 LIG1 -0.8690
7 H21 5.3192 -7.5493 61.0935 H 1 LIG1 0.4000
8 C15 4.0237 -6.1762 62.1229 C.3 1 LIG1 0.3690
9 H151 3.8939 -5.0973 61.9870 H 1 LIG1 0.0000
10 H152 3.2193 -6.6413 61.5447 H 1 LIG1 0.0000
11 C17 3.8736 -6.5912 63.5924 C.3 1 LIG1 0.2700
12 H171 4.6596 -6.1445 64.2086 H 1 LIG1 0.0000
13 H172 3.9921 -7.6769 63.6743 H 1 LIG1 0.0000
14 N4 2.5639 -6.2221 64.1353 N.3 1 LIG1 -0.9900
15 H41 2.4577 -6.6159 65.0700 H 1 LIG1 0.3600
16 H42 2.4917 -5.2108 64.2652 H 1 LIG1 0.3600
17 C1 7.7002 -6.3956 60.9927 C.ar 1 LIG1 0.0860
18 C2 8.9082 -5.6872 61.1019 C.ar 1 LIG1 0.0860
19 C8 8.9765 -4.4812 61.8191 C.ar 1 LIG1 0.1000
20 N3 10.1738 -3.7209 61.8975 N.pl3 1 LIG1 -0.8690
21 H31 11.0225 -4.1407 61.5139 H 1 LIG1 0.4000
22 C14 10.2571 -2.3301 62.3616 C.3 1 LIG1 0.3690
23 H141 9.7075 -2.1856 63.2971 H 1 LIG1 0.0000
24 H142 11.3055 -2.1195 62.5967 H 1 LIG1 0.0000
25 C16 9.7871 -1.3637 61.2695 C.3 1 LIG1 0.2700
26 H161 8.7538 -1.5816 60.9889 H 1 LIG1 0.0000
27 H162 10.3909 -1.5073 60.3677 H 1 LIG1 0.0000
28 N5 9.8936 0.0332 61.6925 N.3 1 LIG1 -0.9900
29 H51 9.2225 0.2326 62.4380 H 1 LIG1 0.3600
30 H52 9.6396 0.6456 60.9184 H 1 LIG1 0.3600
31 C4 10.1364 -6.2108 60.4346 C.2 1 LIG1 0.3980
32 O2 11.2530 -5.7654 60.6707 O.2 1 LIG1 -0.5700
33 C6 10.0141 -7.2971 59.4490 C.ar 1 LIG1 0.0860
34 C12 11.0881 -7.6594 58.6443 C.ar 1 LIG1 -0.1500
35 H121 12.0562 -7.1731 58.7178 H 1 LIG1 0.1500
36 C13 10.8897 -8.6631 57.7156 C.ar 1 LIG1 0.1600
37 H131 11.7004 -8.9710 57.0655 H 1 LIG1 0.1500
38 N1 9.7291 -9.3166 57.5349 N.ar 1 LIG1 -0.6200
39 C11 8.7269 -8.9666 58.3545 C.ar 1 LIG1 0.1600
40 H111 7.8133 -9.5269 58.2104 H 1 LIG1 0.1500
41 C5 8.8179 -7.9675 59.3109 C.ar 1 LIG1 0.0860
42 C3 7.6606 -7.6316 60.1569 C.2 1 LIG1 0.3980
43 O1 6.6912 -8.3797 60.1344 O.2 1 LIG1 -0.5700
@<TRIPOS>BOND
1 1 2 1
2 2 3 2
3 2 19 1
4 3 4 1
5 3 5 1
6 5 6 1
7 5 17 2
8 6 7 1
9 6 8 1
10 8 9 1
11 8 10 1
12 8 11 1
13 11 12 1
14 11 13 1
15 11 14 1
16 14 15 1
17 14 16 1
18 17 18 1
19 17 42 1
20 18 19 2
21 18 31 1
22 19 20 1
23 20 21 1
24 20 22 1
25 22 23 1
26 22 24 1
27 22 25 1
28 25 26 1
29 25 27 1
30 25 28 1
31 28 29 1
32 28 30 1
33 31 32 2
34 31 33 1
35 33 34 1
36 33 41 2
37 34 35 1
38 34 36 2
39 36 37 1
40 36 38 1
41 38 39 2
42 39 40 1
43 39 41 1
44 41 42 1
45 42 43 2
@<TRIPOS>SUBSTRUCTURE
1 LIG1 1
@<TRIPOS>CRYSIN
90.1590 90.1590 90.1590 90.0000 90.0000 90.0000 0 0
LIG.str
* Toppar stream file generated by
* CHARMM General Force Field (CGenFF) program version 2.5
* For use with CGenFF version 4.5
*
read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 2.5
*
36 1
! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.
RESI LIG 0.000 ! param penalty= 45.000 ; charge penalty= 30.477
GROUP ! CHARGE CH_PENALTY
ATOM H91 HGR61 0.115 ! 0.000
ATOM C9 CG2R61 -0.112 ! 0.000
ATOM C10 CG2R61 -0.112 ! 0.000
ATOM H101 HGR61 0.115 ! 0.000
ATOM C7 CG2R61 -0.020 ! 16.260
ATOM N2 NG311 -0.553 ! 25.251
ATOM H21 HGPAM1 0.371 ! 0.000
ATOM C15 CG321 -0.011 ! 14.138
ATOM H151 HGA2 0.090 ! 0.000
ATOM H152 HGA2 0.090 ! 0.000
ATOM C17 CG321 0.083 ! 17.378
ATOM H171 HGA2 0.090 ! 0.000
ATOM H172 HGA2 0.090 ! 0.000
ATOM N4 NG321 -0.877 ! 12.523
ATOM H41 HGPAM2 0.319 ! 0.000
ATOM H42 HGPAM2 0.319 ! 0.000
ATOM C1 CG2R61 0.020 ! 26.841
ATOM C2 CG2R61 0.020 ! 26.841
ATOM C8 CG2R61 -0.020 ! 16.260
ATOM N3 NG311 -0.553 ! 25.251
ATOM H31 HGPAM1 0.371 ! 0.000
ATOM C14 CG321 -0.011 ! 14.138
ATOM H141 HGA2 0.090 ! 0.000
ATOM H142 HGA2 0.090 ! 0.000
ATOM C16 CG321 0.083 ! 17.378
ATOM H161 HGA2 0.090 ! 0.000
ATOM H162 HGA2 0.090 ! 0.000
ATOM N5 NG321 -0.877 ! 12.523
ATOM H51 HGPAM2 0.319 ! 0.000
ATOM H52 HGPAM2 0.319 ! 0.000
ATOM C4 CG2O5 0.424 ! 30.477
ATOM O2 OG2D3 -0.459 ! 0.000
ATOM C6 CG2R61 0.015 ! 21.571
ATOM C12 CG2R61 -0.114 ! 1.700
ATOM H121 HGR61 0.115 ! 0.000
ATOM C13 CG2R61 0.182 ! 0.000
ATOM H131 HGR62 0.122 ! 0.000
ATOM N1 NG2R60 -0.603 ! 0.000
ATOM C11 CG2R61 0.181 ! 1.700
ATOM H111 HGR62 0.120 ! 0.000
ATOM C5 CG2R61 0.022 ! 21.571
ATOM C3 CG2O5 0.426 ! 30.477
ATOM O1 OG2D3 -0.459 ! 0.000
BOND H91 C9
BOND C9 C10
BOND C9 C8
BOND C10 H101
BOND C10 C7
BOND C7 N2
BOND C7 C1
BOND N2 H21
BOND N2 C15
BOND C15 H151
BOND C15 H152
BOND C15 C17
BOND C17 H171
BOND C17 H172
BOND C17 N4
BOND N4 H41
BOND N4 H42
BOND C1 C2
BOND C1 C3
BOND C2 C8
BOND C2 C4
BOND C8 N3
BOND N3 H31
BOND N3 C14
BOND C14 H141
BOND C14 H142
BOND C14 C16
BOND C16 H161
BOND C16 H162
BOND C16 N5
BOND N5 H51
BOND N5 H52
BOND C4 O2
BOND C4 C6
BOND C6 C12
BOND C6 C5
BOND C12 H121
BOND C12 C13
BOND C13 H131
BOND C13 N1
BOND N1 C11
BOND C11 H111
BOND C11 C5
BOND C5 C3
BOND C3 O1
IMPR C4 C2 C6 O2
IMPR C3 C1 C5 O1
END
read param card flex append
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 2.5
*
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.
BONDS
ANGLES
CG2R61 CG2O5 CG2R61 40.00 117.20 ! LIG , from CG2O3 CG2O5 CG2R61, penalty= 34
DIHEDRALS
CG2R61 CG2O5 CG2R61 CG2R61 1.5850 2 180.00 ! LIG , from CG2O3 CG2O5 CG2R61 CG2R61, penalty= 34
CG2O5 CG2R61 CG2R61 CG2O5 3.1000 2 180.00 ! LIG , from CG2O5 CG2R61 CG2R61 CG2R61, penalty= 45
CG2O5 CG2R61 CG2R61 NG311 3.1000 2 180.00 ! LIG , from CG2R61 CG2R61 CG2R61 NG311, penalty= 45
NG311 CG321 CG321 NG321 0.3000 3 0.00 ! LIG , from CG321 CG321 CG321 NG311, penalty= 39
CG321 CG321 NG311 CG2R61 0.8000 1 180.00 ! LIG , from CG321 CG321 NG311 CG2R64, penalty= 4
CG321 CG321 NG311 CG2R61 1.1000 3 0.00 ! LIG , from CG321 CG321 NG311 CG2R64, penalty= 4
IMPROPERS
CG2O5 CG2R61 CG2R61 OG2D3 72.0000 0 0.00 ! LIG , from CG2O5 CG2O3 CG2R61 OG2D3, penalty= 19
END
RETURN
LIG.gro
GROningen MAchine for Chemical Simulation
43
1LIG H91 1 0.779 -0.312 6.299
1LIG C9 2 0.781 -0.404 6.242
1LIG C10 3 0.663 -0.475 6.234
1LIG H101 4 0.577 -0.433 6.285
1LIG C7 5 0.653 -0.594 6.164
1LIG N2 6 0.530 -0.664 6.156
1LIG H21 7 0.532 -0.755 6.109
1LIG C15 8 0.402 -0.618 6.212
1LIG H151 9 0.389 -0.510 6.199
1LIG H152 10 0.322 -0.664 6.155
1LIG C17 11 0.387 -0.659 6.359
1LIG H171 12 0.466 -0.614 6.421
1LIG H172 13 0.399 -0.768 6.367
1LIG N4 14 0.256 -0.622 6.413
1LIG H41 15 0.246 -0.662 6.507
1LIG H42 16 0.249 -0.521 6.426
1LIG C1 17 0.770 -0.640 6.099
1LIG C2 18 0.891 -0.569 6.110
1LIG C8 19 0.898 -0.448 6.182
1LIG N3 20 1.017 -0.372 6.190
1LIG H31 21 1.102 -0.414 6.151
1LIG C14 22 1.026 -0.233 6.236
1LIG H141 23 0.971 -0.219 6.330
1LIG H142 24 1.131 -0.212 6.260
1LIG C16 25 0.979 -0.136 6.127
1LIG H161 26 0.875 -0.158 6.099
1LIG H162 27 1.039 -0.151 6.037
1LIG N5 28 0.989 0.003 6.169
1LIG H51 29 0.922 0.023 6.244
1LIG H52 30 0.964 0.065 6.092
1LIG C4 31 1.014 -0.621 6.043
1LIG O2 32 1.125 -0.576 6.067
1LIG C6 33 1.001 -0.730 5.945
1LIG C12 34 1.109 -0.766 5.864
1LIG H121 35 1.206 -0.717 5.872
1LIG C13 36 1.089 -0.866 5.772
1LIG H131 37 1.170 -0.897 5.707
1LIG N1 38 0.973 -0.932 5.753
1LIG C11 39 0.873 -0.897 5.835
1LIG H111 40 0.781 -0.953 5.821
1LIG C5 41 0.882 -0.797 5.931
1LIG C3 42 0.766 -0.763 6.016
1LIG O1 43 0.669 -0.838 6.013
0.00000 0.00000 0.00000
LIG.prm
[ bondtypes ]
; i j func b0 kb
[ angletypes ]
; i j k func theta0 ktheta ub0 kub
CG2R61 CG2O5 CG2R61 5 117.200000 334.720000 0.00000000 0.00
[ dihedraltypes ]
; i j k l func phi0 kphi mult
CG2R61 CG2O5 CG2R61 CG2R61 9 180.000000 6.631640 2
CG2O5 CG2R61 CG2R61 CG2O5 9 180.000000 12.970400 2
CG2O5 CG2R61 CG2R61 NG311 9 180.000000 12.970400 2
NG311 CG321 CG321 NG321 9 0.000000 1.255200 3
CG321 CG321 NG311 CG2R61 9 180.000000 3.347200 1
CG321 CG321 NG311 CG2R61 9 0.000000 4.602400 3
[ dihedraltypes ]
; 'improper' dihedrals
; i j k l func phi0 kphi
CG2O5 CG2R61 CG2R61 OG2D3 2 0.000000 602.496000
Thank you very much for your response.
Regards
Hemant