VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 25 2011 - 13:16:32 CST

On Fri, Nov 25, 2011 at 1:16 PM, Ban Arn <ban.arn_at_gmail.com> wrote:
> 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.

you appear to be counting the number of atoms,
not the number of water molecules. try dividing by 3.

axel.

>
> Many Thanks
> Balaji
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.