Re: [AMBER] Implicit solvent and membrane protein

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Thu, 17 Jul 2014 11:27:50 -0700

I think the only IS model supporting membrane proteins up to amber14
is the pb model with appropriate options set up. It doesn't work with
MD, only for mmpbsa type of jobs.

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Thu, Jul 17, 2014 at 12:21 AM, James Starlight
<jmsstarlight.gmail.com> wrote:
> Dear Amber users!
>
> I'd like to use some IS  amber model for the simulation of the membrane
> protein. In particular I'd like to do NVT simulation with the applied
> position restraints on all secondary structure elements of my protein (to
> prevent conformation changes in its)
>
>   restraint_wt=10.0,
> restraintmask=':6-33,40-68,76-109,120-143,177-204,216-246,256-286',
>
> to refine only flexible loop parts of my model
>
> I'll be very thankful if someone have made simulation of any membrane
> proteins using one of the gb models and could give me some suggestions
> regarding most suitable gb model for this case.
>
>
> James
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Received on Thu Jul 17 2014 - 11:30:02 PDT