VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Fri Nov 30 2007 - 09:14:11 CST

Hi Pavan,
I'm sorry, my previous description wasn't definite. Well, I have written 2
scripts which can reduce the size of a trajectory in 2 slightly different ways.
The one takes a cuttof value, looks in each frame which atoms are within that
cuttof and keeps only them (so the atom number in the final trajectory may
vary- I don't I advise you to use it on big trajectories). The other one which
I thinks suits better to your case, takes a water number N and keeps anly the N
closest waters. You can also define how many non-water hetero compounds you want
in each frame or let the program choose the minimum required number. Finaly you
have the option to define a smaller fragment of your macromolecule (i.e.
residues 1 to 50) and the program will find and keep only the N closest to that
fragment waters.
I suggest you have a look at this:

https://biocore-s.ks.uiuc.edu/biocore/secure/biofs/biofs.do?directory=/VMD%20(Public)/src/truncate_trajectory/

The script you want is called "truncate_trajectory". I have also a documents
with instructions which has an example.
regards,
Thomas

Αρχικό μήνυμα από Pavan Ghatty <pavan.vmd_at_gmail.com>:

> 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
> > >
> >
> >
> >
> >
>