VMD-L Mailing List

From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Fri Oct 14 2016 - 08:36:56 CDT

Dear All,

I want to calculate the surface area change of protein on graphene surface with respect to timescale. i used sasa for this approach and I have modified previously available script as below.

Please suggest if, this script is correct or wrong:

#sasa_complex
puts -nonewline "\n \t \t Selection: "
#gets stdin selmode
# selection
set sel [atomselect top all]
set A [atomselect top "protein"] #for the protein above graphene sheet
set B [atomselect top "segname CCC"] #for graphene sheet below protein
set n [molinfo top get numframes]
set s 500
set output [open "sasa_complex.dat" w]
# sasa calculation loop
for {set i 0} {$i < $n} {incr i} {
molinfo top set frame $i
set sasa [expr {([measure sasa 1.4 $A -samples $s] + [measure sasa 1.4 $B -samples $s] - [measure sasa 1.4 $sel -samples $s]) * 0.5}]
puts "\t \t progress: $i/$n"
puts $output "$sasa"
}
puts "\t \t progress: $n/$n"
puts "Done."
puts "output file: sasa_complex.dat"
close $output

Looking forward for your suggestions.

Thanks

Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong