Re: [AMBER] GPI-anchor protein cleavage

From: Aditya Padhi <>
Date: Wed, 17 Jun 2015 19:48:58 +0530

Hi Jason,

I do understand what you are saying but there is one more of difficulty
that my protein of interest is a 6-transmembrane protein and its structure
is not known at all. So, an explicit membrane environment could be
necessary for my protein of interest but not essentially for the GPI-anchor
proteins. This problem therefore looks more challenging and I am not sure
how far I can go with this.

Thank you for your comments and suggestions,

On Wed, Jun 17, 2015 at 7:41 AM, Jason Swails <>

> On Tue, Jun 16, 2015 at 6:36 PM, Aditya Padhi <> 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
> _______________________________________________
> AMBER mailing list

Aditya Kumar Padhi, PhD
Kusuma School of Biological Sciences (SBS)
Indian Institute of Technology Delhi
New Delhi-110016, India
Contact no:+91-9711539958
AMBER mailing list
Received on Wed Jun 17 2015 - 07:30:03 PDT
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