VMD-L Mailing List

From: PARMINDER MANKOO (pmankoo1_at_jhu.edu)
Date: Wed Sep 26 2007 - 13:40:12 CDT

Hello,

I want to calculate the surface area of only LYS residue out of total protein and want to get the time series of it. How can I do it? How can I modify the following script for time?

Thanks, Preeti

set outfile [open sasa.dat w]
set allsel [atomselect top "resid 217 to 393 and resname LYS"]
set residlist [lsort -unique [$allsel get residue]]

for {set i 0} { $i < [ $allsel num ] } {incr i } {
    foreach r $residlist {
        set sel [atomselect top "residue $r"]
        set rsasa [measure sasa 1.4 $allsel -restrict $sel]
        $sel set user $rsasa
        $sel delete
        puts $outfile "[residue $r, sasa: $rsasa, time $i]"
    }
}
close $outfile