AMBER Archive (2009)

Subject: Re: [AMBER] PTRAJ: solvent accessible surface area

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jan 14 2009 - 09:00:59 CST

another possibility is to use sander and read the trajectory file as
input and set surften=1, but you'd need to midify the code slightly to
get per-residues info.

On Wed, Jan 14, 2009 at 9:59 AM, <steinbrt_at_rci.rutgers.edu> wrote:
> Hi,
>
>> Can I use ptraj to extract the solvent accessible surface area changes of
>> a residues during the stimulation from mdcrd files?
>
> I dont think ptraj can do this but amber comes with the molsurf program
> that computes SASAs. You would have to transform your mdcrd into a series
> of pqr-files for your residue, which wouldnt be hard to do by hand, or
> have MM-PBSA do it... Unless your residue is partially buried in some
> macromolecule, in which case it might become more tricky...
>
> Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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