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, [email protected] wrote:
Part 1.2
Subject:
[gmx-users] swiss param query,
From:
ram bio <[email protected]>
Date:
Tue, 12 Oct 2010 16:32:39 +0200
To:
Discussion list for GROMACS users <[email protected]>
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.
[email protected] http://folding.bmc.uu.se
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