AMBER Archive (2009)

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

From: steinbrt_at_rci.rutgers.edu
Date: Wed Jan 14 2009 - 08:59:19 CST

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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