[gmx-users] Using ffgmx and ffG43a1 topologies

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Apr 7 11:31:54 CEST 2007

Hi Venky,

You may be able to map to map the parameters from ffgmx to ffg43a1,
looking at the force field files ffgmx* and ffG43a1*, but that does
not guarantee in any way that your results will make any sense.
Especially since the SDS makes up an important part of your system,
you have to make sure the parameters for that part are reasonable (the
least). You can try the prodrg parameters and simulate SDS, checking
against available experimental data. I would strongly suggest not just
to take the prodrg parameters and put blind trust in them.



On 4/7/07, Venky Krishna <venky.agas at gmail.com> wrote:
> Hi gmx-users,
> I am trying to simulate a membrane protein covalently attached to a spin
> label in SDS micelle. I have obtained parameters from PRODRG server for SDS
> coordinates which are for use with GROMACS ff (ffgmx)... and my spin label
> forcefield parameters is in GROMOS96 (ffG43a1). My question is, can I use
> the GROMACS parameters of SDS molecules to directly derive its GROMOS96
> params? If so how?
> P.S. If anybody has GROMOS96, SDS ff already, please help! You contribution
> will be much appreciated!
> Thanks
> Venky
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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