[gmx-users] Topology file error for a ligand
Justin A. Lemkul
jalemkul at vt.edu
Mon Nov 23 16:20:56 CET 2009
Anirban Ghosh wrote:
> Thanks a lot Mark and Justin for your replies.
>
> If PRODRG results have to be taken with a pinch of salt, then can you
> please suggest me how to get the proper topology for my ligand, just
> hints. In particular the .itp file is missing the HZ, HB2 and HB3
> hydrogen atoms, which are present in the PDB and GRO files. But the
> other hydrogen atoms are defined properly. Any suggestion is welcome.
>
The missing atoms are not there likely because they are not required. Please
see the following:
http://www.gromacs.org/Documentation/Terminology/Force_Fields/United_Atom_Force_Field
As for derivation of parameters:
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
>
> Regards,
>
>
> Anirban
>
>
> On Mon, Nov 23, 2009 at 5:31 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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--
========================================
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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