Dear All:
I am using GROMACS 4 to do MD simulations of protein-ligand
complexes.I encountered some
problems when generating the topology file of the ligands. I generate
the topology file
of ligands by using topolbuild package. The atom types of GAFF force
field are assigned
to the atoms of the ligand. However, when I used grompp command to
write the tpr file.
There is an error saying:
Fatal error:
Atomtype c3 not found
For more information and tips for troubleshooting, please check the GROMACS
It seemed that, the amber ff03 force field in gromacs 4 didn't include
the atom types of
the GAFF force field.
Does any one have ever encountered the same problem? What can I do to
solve this problem?
this is the topology file of my ligand
_____________________________________________________________________________-
[ moleculetype ]
; Name nrexcl
solute 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB
1 c3 1 DRG C12 1 0.11235 12.000000
2 hx 1 DRG H13 2 0.10011 1.000000
3 hx 1 DRG H14 3 0.11263 1.000000
4 c3 1 DRG C15 4 -0.02190 12.000000
5 c3 1 DRG C4 5 -0.09576 12.000000
6 hc 1 DRG H5 6 0.10817 1.000000
7 hc 1 DRG H6 7 0.05611 1.000000
8 hc 1 DRG H16 8 0.11695 1.000000
9 n4 1 DRG N10 9 -0.75781 14.000000
10 hn 1 DRG H11 10 0.44475 1.000000
11 hn 1 DRG HN2 11 0.45369 1.000000
12 c3 1 DRG C7 12 0.11240 12.000000
13 hx 1 DRG H8 13 0.10008 1.000000
14 hx 1 DRG H9 14 0.11262 1.000000
15 c3 1 DRG C2 15 -0.02192 12.000000
16 hc 1 DRG H3 16 0.11695 1.000000
17 ca 1 DRG C1 17 -0.13377 12.000000
18 ca 1 DRG C22 18 -0.10700 12.000000
19 ha 1 DRG H23 19 0.16944 1.000000
20 ca 1 DRG C17 20 -0.13377 12.000000
21 ca 1 DRG C18 21 -0.10699 12.000000
22 ha 1 DRG H19 22 0.16945 1.000000
23 ca 1 DRG C20 23 0.28871 12.000000
24 ca 1 DRG C21 24 0.28875 12.000000
25 nb 1 DRG N29 25 -0.61584 14.000000
26 ca 1 DRG C27 26 0.31853 12.000000
27 h4 1 DRG H28 27 0.05520 1.000000
28 ca 1 DRG C25 28 0.31854 12.000000
29 h4 1 DRG H26 29 0.05519 1.000000
30 nb 1 DRG N24 30 -0.61586 14.000000
[ bonds ]
; ai aj funct r k
28 29 1 1.0880e-01 2.8694e+05
26 27 1 1.0880e-01 2.8694e+05
21 22 1 1.0870e-01 2.8811e+05
18 19 1 1.0870e-01 2.8811e+05
15 16 1 1.0920e-01 2.8225e+05
12 13 1 1.0910e-01 2.8342e+05
12 14 1 1.0910e-01 2.8342e+05
9 10 1 1.0330e-01 3.0878e+05
9 11 1 1.0330e-01 3.0878e+05
5 6 1 1.0920e-01 2.8225e+05
5 7 1 1.0920e-01 2.8225e+05
4 8 1 1.0920e-01 2.8225e+05
1 2 1 1.0910e-01 2.8342e+05
1 3 1 1.0910e-01 2.8342e+05
28 30 1 1.3420e-01 4.0426e+05
26 28 1 1.3870e-01 4.0033e+05
25 26 1 1.3420e-01 4.0426e+05
24 25 1 1.3420e-01 4.0426e+05
23 24 1 1.3870e-01 4.0033e+05
23 30 1 1.3420e-01 4.0426e+05
21 23 1 1.3870e-01 4.0033e+05
20 21 1 1.3870e-01 4.0033e+05
18 24 1 1.3870e-01 4.0033e+05
17 18 1 1.3870e-01 4.0033e+05
17 20 1 1.3870e-01 4.0033e+05
15 17 1 1.5130e-01 2.7070e+05
12 15 1 1.5350e-01 2.5363e+05
9 12 1 1.4990e-01 2.4568e+05
5 15 1 1.5350e-01 2.5363e+05
4 5 1 1.5350e-01 2.5363e+05
4 20 1 1.5130e-01 2.7070e+05
1 4 1 1.5350e-01 2.5363e+05
1 9 1 1.4990e-01 2.4568e+05
[ pairs ]
; ai aj funct
27 29 1
27 30 1
25 29 1
24 27 1
23 29 1
22 24 1
22 30 1
19 20 1
19 23 1
19 25 1
17 22 1
16 18 1
16 20 1
15 19 1
14 16 1
14 17 1
13 16 1
13 17 1
11 13 1
11 14 1
11 15 1
10 13 1
10 14 1
10 15 1
9 16 1
9 8 1
8 15 1
8 17 1
8 21 1
7 8 1
7 20 1
7 12 1
7 16 1
7 17 1
6 8 1
6 20 1
6 12 1
6 16 1
6 17 1
5 13 1
5 14 1
4 10 1
4 11 1
4 16 1
4 22 1
3 5 1
3 8 1
3 20 1
3 10 1
3 11 1
3 12 1
2 5 1
2 8 1
2 20 1
2 10 1
2 11 1
2 12 1
1 6 1
1 7 1
1 13 1
1 14 1
25 30 1
24 28 1
23 26 1
21 25 1
21 28 1
20 24 1
20 30 1
18 21 1
18 30 1
18 26 1
17 23 1
17 25 1
15 24 1
15 21 1
12 18 1
12 20 1
9 20 1
9 17 1
9 5 1
5 21 1
5 18 1
4 12 1
4 18 1
4 23 1
1 15 1
1 17 1
1 21 1
[ angles ]
; ai aj ak funct theta cth
29 28 30 1 1.1594e+02 4.3346e+02
27 26 28 1 1.2109e+02 4.0334e+02
26 28 29 1 1.2109e+02 4.0334e+02
25 26 27 1 1.1594e+02 4.3346e+02
22 21 23 1 1.2001e+02 4.0585e+02
20 21 22 1 1.2001e+02 4.0585e+02
19 18 24 1 1.2001e+02 4.0585e+02
17 18 19 1 1.2001e+02 4.0585e+02
16 15 17 1 1.1015e+02 3.9330e+02
14 12 15 1 1.1174e+02 3.8493e+02
13 12 14 1 1.1074e+02 3.2635e+02
13 12 15 1 1.1174e+02 3.8493e+02
12 15 16 1 1.1005e+02 3.8828e+02
11 9 12 1 1.1011e+02 3.8660e+02
10 9 11 1 1.0811e+02 3.3890e+02
10 9 12 1 1.1011e+02 3.8660e+02
9 12 13 1 1.0791e+02 4.1003e+02
9 12 14 1 1.0791e+02 4.1003e+02
8 4 20 1 1.1015e+02 3.9330e+02
7 5 15 1 1.1005e+02 3.8828e+02
6 5 7 1 1.0835e+02 3.2970e+02
6 5 15 1 1.1005e+02 3.8828e+02
5 4 8 1 1.1005e+02 3.8828e+02
5 15 16 1 1.1005e+02 3.8828e+02
4 5 6 1 1.1005e+02 3.8828e+02
4 5 7 1 1.1005e+02 3.8828e+02
3 1 4 1 1.1174e+02 3.8493e+02
3 1 9 1 1.0791e+02 4.1003e+02
2 1 3 1 1.1074e+02 3.2635e+02
2 1 4 1 1.1174e+02 3.8493e+02
2 1 9 1 1.0791e+02 4.1003e+02
1 4 8 1 1.1005e+02 3.8828e+02
1 9 10 1 1.1011e+02 3.8660e+02
1 9 11 1 1.1011e+02 3.8660e+02
26 28 30 1 1.2263e+02 5.7907e+02
25 26 28 1 1.2263e+02 5.7907e+02
24 23 30 1 1.2263e+02 5.7907e+02
24 25 26 1 1.1586e+02 5.7404e+02
23 24 25 1 1.2263e+02 5.7907e+02
23 30 28 1 1.1586e+02 5.7404e+02
21 23 24 1 1.1997e+02 5.6233e+02
21 23 30 1 1.2263e+02 5.7907e+02
20 21 23 1 1.1997e+02 5.6233e+02
18 17 20 1 1.1997e+02 5.6233e+02
18 24 23 1 1.1997e+02 5.6233e+02
18 24 25 1 1.2263e+02 5.7907e+02
17 18 24 1 1.1997e+02 5.6233e+02
17 20 21 1 1.1997e+02 5.6233e+02
15 17 18 1 1.2063e+02 5.3388e+02
15 17 20 1 1.2063e+02 5.3388e+02
12 15 17 1 1.1461e+02 5.2300e+02
9 12 15 1 1.0893e+02 5.5229e+02
5 4 20 1 1.1461e+02 5.2300e+02
5 15 12 1 1.1063e+02 5.2886e+02
5 15 17 1 1.1461e+02 5.2300e+02
4 1 9 1 1.0893e+02 5.5229e+02
4 5 15 1 1.1063e+02 5.2886e+02
4 20 17 1 1.2063e+02 5.3388e+02
4 20 21 1 1.2063e+02 5.3388e+02
1 4 5 1 1.1063e+02 5.2886e+02
1 4 20 1 1.1461e+02 5.2300e+02
1 9 12 1 1.1064e+02 5.2551e+02
[ dihedrals ]
;i j k l func C0 ... C5
27 26 28 29 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
27 26 28 30 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
25 26 28 29 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
24 25 26 27 3 40.16640 0.00000 -40.16640
0.00000 0.00000 0.00000 ;
23 30 28 29 3 40.16640 0.00000 -40.16640
0.00000 0.00000 0.00000 ;
22 21 23 24 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
22 21 23 30 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
19 18 17 20 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
19 18 24 23 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
19 18 24 25 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
17 20 21 22 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
16 15 17 18 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
16 15 17 20 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
15 17 18 19 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
14 12 15 16 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
14 12 15 17 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
13 12 15 16 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
13 12 15 17 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
11 9 12 13 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
11 9 12 14 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
11 9 12 15 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
10 9 12 13 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
10 9 12 14 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
10 9 12 15 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
9 12 15 16 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
9 1 4 8 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
8 4 5 15 3 0.66944 2.00832 0.00000
-2.67776 0.00000 0.00000 ;
8 4 20 17 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
8 4 20 21 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
7 5 4 8 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ;
7 5 4 20 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
7 5 15 12 3 0.66944 2.00832 0.00000
-2.67776 0.00000 0.00000 ;
7 5 15 16 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ;
7 5 15 17 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
6 5 4 8 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ;
6 5 4 20 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
6 5 15 12 3 0.66944 2.00832 0.00000
-2.67776 0.00000 0.00000 ;
6 5 15 16 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ;
6 5 15 17 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
5 15 12 13 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
5 15 12 14 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
4 1 9 10 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
4 1 9 11 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
4 5 15 16 3 0.66944 2.00832 0.00000
-2.67776 0.00000 0.00000 ;
4 20 21 22 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
3 1 4 5 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
3 1 4 8 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
3 1 4 20 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
3 1 9 10 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
3 1 9 11 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
3 1 9 12 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
2 1 4 5 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
2 1 4 8 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
2 1 4 20 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
2 1 9 10 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
2 1 9 11 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
2 1 9 12 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
1 4 5 6 3 0.66944 2.00832 0.00000
-2.67776 0.00000 0.00000 ;
1 4 5 7 3 0.66944 2.00832 0.00000
-2.67776 0.00000 0.00000 ;
1 9 12 13 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
1 9 12 14 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
26 29 28 30 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
28 27 26 25 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
20 23 21 22 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
17 24 18 19 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
25 24 23 30 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
25 26 28 30 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
24 23 30 28 3 40.16640 0.00000 -40.16640
0.00000 0.00000 0.00000 ;
24 25 26 28 3 40.16640 0.00000 -40.16640
0.00000 0.00000 0.00000 ;
23 24 25 26 3 40.16640 0.00000 -40.16640
0.00000 0.00000 0.00000 ;
23 30 28 26 3 40.16640 0.00000 -40.16640
0.00000 0.00000 0.00000 ;
21 23 24 25 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
21 23 30 28 3 40.16640 0.00000 -40.16640
0.00000 0.00000 0.00000 ;
20 17 18 24 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
20 21 23 24 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
20 21 23 30 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
18 17 20 21 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
18 24 23 21 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
18 24 23 30 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
18 24 25 26 3 40.16640 0.00000 -40.16640
0.00000 0.00000 0.00000 ;
17 18 24 23 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
17 18 24 25 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
17 20 21 23 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
15 17 18 24 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
15 17 20 21 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
15 5 4 20 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
12 15 17 18 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
12 15 17 20 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
9 1 4 20 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
9 12 15 17 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
9 1 4 5 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
5 4 20 17 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
5 4 20 21 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
5 15 12 9 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
5 15 17 18 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
5 15 17 20 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
4 1 9 12 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
4 5 15 12 3 3.68192 3.09616 -2.09200
-3.01248 0.00000 0.00000 ;
4 5 15 17 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
4 20 17 15 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
4 20 17 18 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
4 20 21 23 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ;
1 4 5 15 3 3.68192 3.09616 -2.09200
-3.01248 0.00000 0.00000 ;
1 4 20 17 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
1 4 20 21 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ;
1 9 12 15 3 0.65270 1.95811 0.00000
-2.61082 0.00000 0.00000 ;
18 23 24 25 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
21 24 23 30 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
17 21 20 4 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
15 18 17 20 3 9.20480 0.00000 -9.20480
0.00000 0.00000 0.00000 ;
___________________________________________________________________________________________________
It seemed that the atoms types in GAFF force field (e.g., c3, hx, hc,
etc. ) can not be recongnized by the amber ff03 FF implemented in
gromacs 4.5.3.
Thanks in advance!!!
R.X.G.
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