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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