VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 01 2011 - 11:33:34 CST

On Tue, Feb 1, 2011 at 11:25 AM, ban arn <ban.arn_at_gmail.com> wrote:
> Dear VMD users,
>
> I tried this command & its works
>
> set sel [atomselect top "water within 3 of resid 293 113"]
> $sel num
>
> It gives number of water molecules for one snapshot.
>
> But, I have to loop over the same to all snap shots & get output as txt file.
>
> I am not familiar with tcl scritping.

if you want to use it, you have to learn it; at least some of it!

the VMD user's guide gives some examples for how to loop
over a trajectory, as do some of the VMD tutorials available
from the VMD home page. please help yourself, they are free
and you'll learn something that will become very useful for
you in the future.

cheers,
    axel.

>
> Kindly advice.
>
> Many Thanks
> Balaji
>
>
>
> On Tue, Feb 1, 2011 at 4:12 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>> Hi Balaji,
>>
>> Try something like this in the console:
>> [atomselect top "name OH2 and same residue as within 4 of protein"] num
>>
>> Cheers,
>> Jerome
>>
>> On 1 February 2011 15:56, ban arn <ban.arn_at_gmail.com> wrote:
>>> Dear VMD users
>>>
>>> I would like to count number of water molecules within the selection
>>> of residues.
>>>
>>> Is there any vmd script available for doing the same for all frames.
>>>
>>> Kindly advice.
>>>
>>> Many Thanks
>>> Balaji
>>>
>>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.