[gmx-users] Topology file error for a ligand
Justin A. Lemkul
jalemkul at vt.edu
Mon Nov 23 13:01:46 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. 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.
This is happening because PRODRG gives GROMOS-compatible topologies. They are
united-atom. So naturally, if you attempt to use an all-atom structure, there
will be mismatch.
I also would not trust the PRODRG topology at face value, as I have posted
across this list dozens of times.
-Justin
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------
> 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
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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