[email protected] wrote:
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?
You need to use atom types that exist in the Gromacs implementation of the Amber
force fields. Probably the missing atomtypes are just named something else in
Gromacs. See $GMXLIB/amber03.ff/atomtypes.atp for acceptable types. Note that
they are case-sensitive, so for example, "hc" is not the same as "HC", etc.
-Justin
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.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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