[gmx-users] Re: swiss param query

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 12 19:27:26 CEST 2010

On 2010-10-12 19.09, Michel Cuendet wrote:
>   Hi Ram,
> Please note that the SwissParam parameters have been tested only with
> the charmm force field. But this in principle shouldn't prevent you from
> TRYING to use these parameters (which come from the Merck Molecular
> Force Field in the first place) with OPLS.
I guess this will be difficult because the mapping of atomtypes from one 
force field to another is not one-to-one.
> The error you mention should not happen, because all atomtypes needed by
> SwissParam should be defined in the ligand.itp file. Are you sure that
> you included the ligand.itp file exactly at the right place in your
> topol.top file? It should be done as suggested in the SwissParam tutorial:
> http://www.swissparam.ch/SwissParam_gromacs_tutorial.html

By the way Michel,

your website looks very interesting. I would like to make this process 
non-interactive, and can generate a mol2 file from a pdb file using 
babel (if the pdb file has H already of course) and hence skip the 
chimera step. I just submitted a molecule but haven't got the result 
yet, is there an off-line version? Or one where I can send 200 molecules?

> If you are still encountering problems, please send me your ligand.itp
> and topol.top files offline.
> Best regards,
> Michel
> On 10/12/2010 11:23 AM, gmx-users-request at gromacs.org wrote:
>> Part 1.2
>> Subject:
>> [gmx-users] swiss param query,
>> From:
>> ram bio <rmbio861 at gmail.com>
>> Date:
>> Tue, 12 Oct 2010 16:32:39 +0200
>> To:
>> Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Dear Gromacs Users,
>> I have generated the topology and parameters files for my ligand
>> through swiss param site. Now i am trying to run a simulation of
>> protein ligand complex in POPC bilayer using OPLS force field in
>> Gromacs, but when I am using the grompp command in gromacs for tpr
>> generation I am getting an error as follows:
>> Atomtype C5A not found
>> Please let me know your suggestions, to correct this error, I have
>> included ligand.itp in the topology file of the protein.
>> Thanks,
>> ram
> ==========================================================
> Michel Cuendet, Ph.D
> Molecular Modeling Group
> Swiss Institute of Bioinformatics
> CH-1015 Lausanne
> Switzerland
> http://lausanne.isb-sib.ch/~mcuendet/
> ==========================================================

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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