[gmx-users] gromos force field in PRODRG server

[Justin Lemkul]

On 6/17/13 9:17 AM, shahab shariati wrote:
> Dear gromacs users
>
>
> I want to do MD simualation for a protein-ligand system.
>
> For ligand, I use PRODRG server. I know that this server generate a *.itp
> file for ligand based on gromos force field.
>
> There are 5 versions for gromos force field (GROMOS96 43a1, GROMOS96 43a2,
> GROMOS96 45a3, GROMOS96 53a5, GROMOS96 53a6)
> in gromacs package.
>
>
> what version of mentioned versions of gromos force field is used in PRODRG
> server to generate a *.itp file for ligand?
>
> In fact, I want to know what version of gromos force fields I should use
> for protein.
>

PRODRG purports to produce parameters compatible with 43A1, but the result is 
very poor (see http://pubs.acs.org/doi/abs/10.1021/ci100335w).  The fact is you 
will have to make so many modifications to a PRODRG-produced topology that you 
can make it compatible with any of the parameter sets, so you should really be 
choosing the force field based on the quality of its representation of the 
protein rather than ease of producing a ligand topology.  ATB is probably a 
better option, but you'll still have to check the parameters (as one always 
should when using servers).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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