VMD-L Mailing List

From: Ban Arn (ban.arn_at_gmail.com)
Date: Fri Nov 25 2011 - 12:16:47 CST

Dear vmd users

I am calculating the number of water molecules present in 3A of some
residues.

This is the script i'm using

set mol [molinfo top]
set out [open result_water_cluster2.txt w]
 set sel [atomselect $mol {same fragment as (water within 2 of protein
(resid 72 376 100 373 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"
}

However the problem is the output of the number of water molecules doesn't
match with visual inspection of trajectories.

Kindly advice me what is going wrong in the script.

Many Thanks
Balaji