[gmx-users] use AMBER ff03 force field in gromacs 4
Justin A. Lemkul
jalemkul at vt.edu
Thu May 12 15:09:08 CEST 2011
mircial at sjtu.edu.cn 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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