VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 21 2009 - 11:21:58 CDT

On Wed, 2009-10-21 at 17:16 +0200, andrea carotti wrote:
> Hi all,

andrea,

> I've this situation: a system already submitted to molecular dynamics
> with Desmond, having 27 organic molecules. With vmd i correctly assigned
> the 27 resid to each mol, but the atom number (index) is the original
> one..so I have some atoms of the same resid jumping in a range 750-777
> and 1099-1150. I would like that for a resid (eg. 1) the range of the
> atoms would be sequential (eg.750-800). Is there the possibility to
> correctly assign the index in vmd according to the resid order?

the index number depends on the _order_ of the atoms in the input.
you cannot reassign it. if the organic molecules are all in one
block, you could try shuffling the residue ids around so that they
are in the order of the atoms.

(please note the difference between "residue" and "resid". the
former, like "index", depends on the order of the residues in
the input and only the latter can be changed).

cheers,
   axel.

> Thanks for your help
> Andrea
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.