[AMBER] SASA

From: Beale, John <John.Beale.stlcop.edu>
Date: Thu, 4 Nov 2010 06:33:43 -0500

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 ph7pcv.nc
strip :WAT
trajout stripped300.mdcrd nobox
EOF

#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?

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
jbeale.stlcop.edu<mailto:jbeale.stlcop.edu>






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Received on Thu Nov 04 2010 - 05:00:03 PDT
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