[gmx-users] Topology file error for a ligand
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Nov 23 12:46:17 CET 2009
Anirban Ghosh wrote:
> Hi ALL,
>
> I want to do a simulation of a protein in presence of a ligand (L-DOPA).
> I am trying to obtain the topology of L-DOPA from the PRODRG server.
> However I am getting an error in the number of atoms in the PDB file
> (with all hydrogens) and the topology parameter file.
If you're saying the coordinate file you get from PRODRG doesn't match
the .itp file you get from PRODRG, then you should take that up with
them. If however they match and you're then running that coordinate file
through pdb2gmx and losing atoms, then read check out
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file
and rethink your workflow.
Mark
> The PDB file
> consists of 25 atoms, but the itp file gives definition for 22 atoms (3
> hydrogens are missing). So every time there is an error w.r.t. number of
> atoms mismatch.
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------
> PDB:
>
> TITLE Gnomes, ROck Monsters And Chili Sauce
> MODEL 1
> ATOM 1 N DAH 1 15.600 17.820 -3.200 1.00 0.00
> ATOM 2 CA DAH 1 16.490 17.500 -2.040 1.00 0.00
> ATOM 3 C DAH 1 18.010 17.580 -2.400 1.00 0.00
> ATOM 4 O DAH 1 18.560 16.790 -3.210 1.00 0.00
> ATOM 5 CB DAH 1 16.100 16.180 -1.290 1.00 0.00
> ATOM 6 CG DAH 1 14.980 16.190 -0.220 1.00 0.00
> ATOM 7 CD1 DAH 1 13.790 16.990 -0.410 1.00 0.00
> ATOM 8 CD2 DAH 1 15.130 15.410 0.970 1.00 0.00
> ATOM 9 CE1 DAH 1 12.770 16.990 0.570 1.00 0.00
> ATOM 10 CE2 DAH 1 14.100 15.400 1.950 1.00 0.00
> ATOM 11 CZ DAH 1 12.900 16.200 1.750 1.00 0.00
> ATOM 12 OE2 DAH 1 14.280 14.630 3.070 1.00 0.00
> ATOM 13 OZ DAH 1 11.880 16.230 2.690 1.00 0.00
> ATOM 14 OXT DAH 1 18.680 18.630 -1.760 1.00 0.00
> ATOM 15 HA DAH 1 16.330 18.300 -1.320 1.00 0.00
> ATOM 16 HB2 DAH 1 15.790 15.470 -2.050 1.00 0.00
> ATOM 17 HB3 DAH 1 17.000 15.790 -0.820 1.00 0.00
> ATOM 18 HD2 DAH 1 16.020 14.820 1.110 1.00 0.00
> ATOM 19 HE1 DAH 1 11.880 17.580 0.420 1.00 0.00
> ATOM 20 HD1 DAH 1 13.670 17.590 -1.300 1.00 0.00
> ATOM 21 HE2 DAH 1 15.190 14.330 3.110 1.00 0.00
> ATOM 22 HZ DAH 1 11.550 15.340 2.820 1.00 0.00
> ATOM 23 H1 DAH 1 15.920 18.680 -3.630 1.00 0.00
> ATOM 24 H2 DAH 1 15.640 17.070 -3.880 1.00 0.00
> ATOM 25 H3 DAH 1 14.650 17.930 -2.880 1.00 0.00
> TER
> ENDMDL
>
> TOPOLOGY FILE:
>
> [ moleculetype ]
> ; Name nrexcl
> DAH 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OM 1 DAH O 1 -0.715 15.9994
> 2 C 1 DAH C 1 0.387 12.0110
> 3 OM 1 DAH OXT 1 -0.716 15.9994
> 4 CH1 1 DAH CA 1 0.178 13.0190
> 5 NL 1 DAH N 1 0.683 14.0067
> 6 H 1 DAH H2 1 0.010 1.0080
> 7 H 1 DAH H3 1 0.010 1.0080
> 8 H 1 DAH H1 1 0.011 1.0080
> 9 CH2 1 DAH CB 1 0.152 14.0270
> 10 C 1 DAH CG 2 -0.020 12.0110
> 11 CR1 1 DAH CD2 2 0.001 12.0110
> 12 HC 1 DAH HD2 2 0.019 1.0080
> 13 C 1 DAH CE2 3 0.130 12.0110
> 14 OA 1 DAH OE2 3 -0.197 15.9994
> 15 H 1 DAH HE2 3 0.051 1.0080
> 16 C 1 DAH CZ 3 0.130 12.0110
> 17 OA 1 DAH OZ 3 -0.197 15.9994
> 18 H 1 DAH HZ 3 0.051 1.0080
> 19 CR1 1 DAH CE1 3 0.001 12.0110
> 20 HC 1 DAH HE1 3 0.031 1.0080
> 21 CR1 1 DAH CD1 4 0.000 12.0110
> 22 HC 1 DAH HD1 4 0.000 1.0080
>
> [ bonds ]...
> -----------------------------------------------------------------------------------------------------------------------------------------------------------
> How can I rectify this issue? Any suggestion is welcome. Thanks a lot.
>
> Regards,
>
> Anirban
>
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