[gmx-users] Re: swiss param query

[Michel Cuendet]

  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.

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

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/
==========================================================
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