From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Thu May 12 2011 - 02:31:16 CDT

Dear All

Thank you for the help. When and if i get this working, i will send an email
back ..

-Maria

On Tue, May 10, 2011 at 5:26 PM, Emmanuel Baribefe Naziga <
baribefe_at_gmail.com> wrote:

> Hi Maria,
>
> If you can convert your trajectory to the AMBER format there is the *
> closest* command in ptraj that can select the closest N waters over the
> course of a simulation. This will give an exact number of water molecules
> but they may not be the same waters over the trajectory.
>
> Ptraj is available for free in the AmberTools package, so you don't need an
> AMBER license. Also I think you can save your trajectory in AMBER format
> (crd or crdbox) in VMD.
>
> Cheers
>
> Emmanuel
>
> On Tue, May 10, 2011 at 8:51 AM, Eduard Schreiner <eschrein_at_ks.uiuc.edu>wrote:
>
>> Hi Maria,
>>
>> I have a proc which will do what you want (ww_nearest.tcl). The file
>> get_closest.tcl shows how it can be used.
>> Note:
>> 1. it is SLOW for large systems and certainly can be improved
>> 2. it's certainly not the best way to do that, but it seems to work
>> for me (I tried it for water and for ions; I did not use it for
>> anything serious, though)
>> 3. it is not extensively tested
>>
>> Check it out and let me know how that works for you.
>>
>> Maybe somebody knows a better way; any suggestions/improvements are
>> appreciated.
>>
>> let me know if you have any trouble with it
>>
>> eddi
>>
>> On Tue, May 10, 2011 at 9:27 AM, maria goranovic
>> <mariagoranovic_at_gmail.com> wrote:
>> > Hi
>> > I know this has been discussed before, but I did not figure out how to
>> reply
>> > to the original thread
>> > So, like many other people here, I want to output a trajectory
>> containing
>> > only water molecules within 5 A of the protein. the obvious problem is
>> that
>> > VMD expects each frame to have exactly the same number of atoms.
>> > However, is there no way to ask vmd to write frames containing the
>> closest N
>> > water molecules to the protein? Has someone written a script for this?
>> > Thank you for helping.
>> > Maria
>> > --
>> > Maria G.
>> > Technical University of Denmark
>> > Copenhagen
>> >
>>
>
>

-- 
Maria G.
Technical University of Denmark
Copenhagen