VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Tue May 10 2011 - 07:03:55 CDT

One way around might be to wrap all the waters back into your system by
using pbc tools, and then do what you are trying below.

Cheers,
Neelanjana

On Tue, May 10, 2011 at 4:17 PM, Aaron Oakley <aarono_at_uow.edu.au> wrote:

> Promblem with that is those waters you select will diffuse away from the
> protein.
> Furthermore, if you reselect every, frame you will get a different number
> of waters
> every frame, with differend residue naumers/segid's. You could write out a
> separate
> PDB file for each selection, but this will take up a lot of space compared
> with a DCD
> file...
> a++
>
> ________________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Jernej Zidar [jernej.zidar_at_gmail.com]
> Sent: Tuesday, 10 May 2011 6:09 PM
> To: VMD list
> Subject: Re: vmd-l: trajectory of water within 5 A of protein
>
> I would use this selection: within 5 of protein (check the syntax)
>
> Then I would save the trajectory with the above selection.
>
> Best,
> Jernej Zidar
>
> On 10.5.2011, at 9:27, maria goranovic 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
>