VMD-L Mailing List

From: Paul R Brenner (pbrenne1_at_nd.edu)
Date: Tue Feb 01 2005 - 13:59:55 CST

Jan,

Thanks for the reply. I am specifically interested in an index for the dihedral
itself (not an index of the atoms which make up the dihedral). I am hoping that
VMD has some way of indexing the dihedrals for a given set of atoms and can
subsequently output them.

Paul

Quoting Jan Saam <saam_at_charite.de>:

> Paul,
>
> I'm not sure, if I di understand you correctly, but I think the answer
> is quite easy:
> If you have an atomselection $sel then you can retrieve the indexes
> either with
> set myindexes [$sel list]
> or
> set myindexes [$sel get index]
>
> if you want them for a specific residue than you have to select
> something like this:
>
> set psiindexes [atomselect top "protein and resid 5 and name N CA"]
> set phiindexes [atomselect top "protein and resid 5 and name CA C"]
>
> Note that vmd outputs the indexxes in ascending order, not in the order
> you typed the atom names. If you need to identify individual indexes
> with atom names you have to select single atoms.
>
> Regards,
> Jan
>
> Paul R Brenner wrote:
> > Is it possible to use VMD to output index information for the dihedrals of
> a
> > molecule. I see that I can use the get function within atomselect to get
> the
> > angle values (phi,psi) but what I am looking for is an index.
> >
> > (I then plan to align these indexes with those assigned by a molecular
> dynamics
> > program to selectively restrict their variation.)
> >
> > Thanks for any pointers,
> >
> > Paul R Brenner
> > Graduate Research Associate
> > Computer Science and Engineering
> > The University of Notre Dame
> >
> >
> >
> >
> >
> >
> >
>