VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Dec 09 2009 - 17:32:07 CST

On Wed, Dec 9, 2009 at 5:30 PM, Bernardo Sosa Padilla Araujo
<bernardospa_at_gmail.com> wrote:
> Hi all,
> I was wondering if any of you had a script or at least any idea about how to
> write one, that can count the number of water molecules around a specific
> part of an enzyme.
> Any suggestions would be greatly appreciated.

bernardo,

what you describe is a not particularly well defined entity.
this kind of counting does not really need a special script,
but needs a well crafted atomselect command and then use
the "num" subcommand to it.

one example would be:
set sel [atomselect top {name OW and water and exwithin 5.0 of protein}]
puts "there are [$sel num] water molecules around all proteins"

for a more detailed help, you need to provide more details on how
you would like to divide the water molecules near the protein into
those that _are_ next to that part and those that are not.

cheers,
    axel.

> Regards,
> Bernardo
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.