From: Jason Swails <>
Date: Thu, 4 Nov 2010 09:13:02 -0400

On Thu, Nov 4, 2010 at 7:33 AM, Beale, John <> wrote:

> I am using the following ptraj script to strip the water from my protein
> system in preparation for calculating the solvent-accessible surface area of
> the system. I use the sander input file below to compute values for ESURF
> over the trajectory.
> #!/bin/csh
> ptraj ph7wat.prmtop << EOF
> trajin
> strip :WAT
> trajout stripped300.mdcrd nobox
> #SASA energy evaluation of the trajectory
> &cntrl
> imin=5, igb=5, gbsa=2,
> ntx=1, maxcyc=0,
> ntc=1, ntf=1,
> ntb=0, ntp=0,
> surften=1,
> ntwe=0, ntpr=500, ntwx=1,
> cut=1000,
> &end
> Does anyone know of a way to alter the ptraj input file to select for a
> single amino acid residue, so that I can monitor SASA of that amino acid vs.
> time?

I don't think the ptraj file is the one you want to alter. All you're using
ptraj for is dumping trajectories, so *selecting* a trajectory means what
exactly? You strip all other residues? If you do that, then the SASA of
that residue will just be its total SASA. I think the best option here is
to use decomposition analysis.

Set idecomp=1 or 2 (the difference is simply whether the 1-4 non-bonded
interactions are added to internal or vdw/eel energy terms, so it doesn't
matter). This will do more or less what you want it to do.

There are also options for doing this with VMD using the "measure sasa"
command. There is some script that automates this, but I can't seem to find
it now.

Good luck!

> Thanks!
> John
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri 63110
> 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Nov 04 2010 - 06:30:02 PDT
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