VMD-L Mailing List

From: Pavan Ghatty (pavan.vmd_at_gmail.com)
Date: Thu Nov 29 2007 - 21:08:06 CST

Hi Thomas,
Your script might not be the best answer to what I want to do but I surely
could use it elsewhere. I use Amber9 for the simulations and I wonder how
the trajectories you propose will work since the number of atoms in every
timestep need not be the same for that kind of a selection.
Thanks,
Pavan Ghatty

On Nov 29, 2007 7:50 PM, Thomas Evangelidis <te8624_at_mbg.duth.gr> wrote:

>
>
> Αρχικό μήνυμα από John Stone <johns_at_ks.uiuc.edu>:
> Hi,
> I may sound boring because I wrote the same things again last week. Are
> you
> interested in reducing the size of your trajectories by keeping only the
> atoms that are within a cuttof distance (you can define this) from your
> macromolecule/s - instead of the x, y and z bounds determined by the
> minmax of
> protein. I have written a tcl script that does this job automatically, if
> you're interested let me know and I'll send it to you.
> regards,
> Thomas
>
>
>
> >
> > Hi,
> > There isn't a selection keyword that performs an axis-aligned bounding
> > box comparison, just the 'within' selection that's a radial distance.
> You
> > could write a script that does this, but a selection by itself won't do
> the
> > job unless your protein remains essentially fixed and the axis-aligned
> > bounding
> > box doesn't move or change size during the simulation.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Nov 29, 2007 at 10:17:51AM -0500, Pavan Ghatty wrote:
> > > Hello All,
> > >
> > > I was wondering if there is an easy way to select water within the x,
> y and
> > > z bounds determined by the minmax of protien for every timestep in
> VMD.
> > >
> > > Thank you,
> > > Pavan Ghatty
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078
> >
>
>
>
>