VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Mon Aug 29 2011 - 04:47:53 CDT

Dear VMD users

I would like to calculate number of water molecules in the binding site for
trajectory.

When i am mentioning the residue id's of bindingsite of protein in the
script, however the script also considers the water molecules number
respectively and doesn't shows me waters in the binding site.

Instead, of that it considers the water ids of trajectory and gives the
count of number of water molecules that are not part of binding site of
protein.

This is the script i'm using...

set mol [molinfo top]
set out [open water_3A.txt w]
set sel [atomselect $mol {water within 3 of resid 82 86 109 110 143 218 220
224 225 228 229 232 233 337 340 and (not waters)} ]
set frames [molinfo $mol get numframes]
for {set i 0} {$i < $frames} {incr i} {
 $sel frame $i
    $sel update
    set n [$sel num]
    puts $out "$i $n"
}

Many Thanks
Balaji