AMBER Archive (2009)
Subject: Re: [AMBER] PTRAJ: solvent accessible surface area
Date: Wed Jan 14 2009 - 08:59:19 CST
> 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...
Dr. Thomas Steinbrecher
610 Taylor Rd.
Piscataway, NJ 08854
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