Re: [AMBER] GPI-anchor protein cleavage

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 16 Jun 2015 20:11:34 -0600

On Tue, Jun 16, 2015 at 6:36 PM, Aditya Padhi <adi.uoh.gmail.com> wrote:

> Dear Jason.
>
> Thank you very much for your detailed reply. I am not new to MD simulations
> and have run simulations before quite extensively.
>
> I wanyed to know if there are any specific forcefields or options in amber
> that I could try as for my protein of interest and the GPI anchor proteins,
> the structures are not available and they are mostly membrane proteins.
>

‚ÄčI don't see why this application would demand a force field that's any
different than what you'd use for other proteins. The structures being
unavailable is a different problem rather orthogonal to force field or
simulation option choices (and obviously one you would have to solve
first). Is this something you'd want to run in a bilayer environment? In
that case, you should include that in your model somehow (and using an
explicit membrane would require you to use a set of lipid and protein force
fields that are compatible; e.g., ff14SB+lipid14 in Amber or CHARMM 36).

Good luck,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 16 2015 - 19:30:02 PDT
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