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

[Justin A. Lemkul]

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

-- 
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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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