VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sun Feb 10 2008 - 17:48:12 CST

Hi again,

For some time I've been measure the SASA by using the following script:

set outfile [open sasa.txt w]
set nf [molinfo top get numframes]
set all [atomselect top "resid 54 to 103"]
for {set i 0} {$i<$nf} {incr i} {
$all frame $i
$all update
set sasa [measure sasa 1.4 $all]
puts $outfile "Frame $i, SASA $sasa"
}
close $outfile

However, I wonder if there is a way to tell VMD to calculate the SASA
using MSMS. I can easily do it using the standalone version of MSMS,
but it'll be nice if I can do it within VMD.

Thanks!
Michel