[gmx-users] Re: Re: swiss param query

[Michel Cuendet]

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-request at gromacs.org wrote:

> From: Michel Cuendet <michel.cuendet at isb-sib.ch>
> Date: 12 octobre 2010 13:09:22 HAE (ÉUA)
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: swiss param query
> Reply-To: Discussion list for GROMACS users <gmx-users at 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-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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