[gmx-users] Retinal and Schiff base parameters for ffG53a6

[KM]

The parameters for ffgmx have been developed by Christian Kandt. I
have it. I need appropriate data specific for G53a6 which is obviously
lacking. Some atom types changed plus there are G53a6 potentials that
need to be added. I could try to add the lacking data e.g. with the
paper of G53a6 developers, however this is something that should be
done by more experienced users, I believe.

Chris

2010/1/11 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> On 1/10/10 6:16 PM, KM wrote:
>>
>> Hello,
>>
>> I would like to simulate bacteriorhodopsin embedded into a membrane. I
>> think ffG53a6 is a good choice - force field is quite new (at least
>> newer than ffgmx) and there are topologies available for the most
>> popular lipids, for example the set developed by Andreas Kukol.
>> To run a simulation I will need parameters for retinal and Schiff base
>> connecting Lys216 with retinal. I have those parameters for ffgmx,
>> however they are incompatible with ffG53a6 (and that's no surprise).
>> Does anyone know where I can get parameters for ffG53a6 force field
>> (or compatible with it)?
>>
>> Chris
>
> If they're not already in the literature or the User Contribution site on
> the Gromacs website, you'll likely have to develop them yourself.  See, for
> example:
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> I know I have seen several simulations of backteriorhodopsin in the
> literature, so perhaps you can find parameters that have already been
> published.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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