Hi all,
Just as a follow-up on this one: the problem was solved by a correct
ordering of the sections in the topology. The SwissParam server (www.swissparam.ch
) works correctly to generate Gromacs topologies for small organic
molecules!
Note that the tutorial has been updated for the case where there is
only one protein chain and no ions in your PDB file (the topol.top
file looks different).
Enjoy,
Michel
On 12 oct. 10, at 14:28, gmx-users-requ...@gromacs.org wrote:
From: Michel Cuendet <michel.cuen...@isb-sib.ch>
Date: 12 octobre 2010 13:09:22 HAE (ÉUA)
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: swiss param query
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
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-requ...@gromacs.org wrote:
Part 1.2
Subject: [gmx-users] swiss param query,
From: ram bio <rmbio...@gmail.com>
Date: Tue, 12 Oct 2010 16:32:39 +0200
To: Discussion list for GROMACS users <gmx-users@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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