VMD-L Mailing List

From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
Date: Thu May 17 2012 - 10:40:25 CDT

Hi,

Have you tried using segname instead of pfrag? I have a feeling that might
do the trick.

cheers,
Grace

On Thu, May 17, 2012 at 8:42 AM, P.-L. Chau <pc104_at_pasteur.fr> wrote:

> Thank you for your message.
>
> > VMD does what *you* ask it to do.
> >
> > [...]
> >
> > VMD is deliberately not trying to be too smart,
> > but rather relies on consistent input data.
> > so if you want scripts to work well, you have
> > to make sure that your selections match the
> > indicators that VMD uses. details on that should
> > all be listed in the user's guide.
>
> Could I ask you if you could possibly be a bit more specific on what I
> should be looking for, please? I have scoured the VMD user's guide, but
> have found precious little about splitting files for preparation for NAMD.
> Would there be some extra tutorial about splitting files and handling ATOM
> and HETATM in pdb files, please?
>
> Thank you very much!
>
> P-L Chau
>
> email: pc104_at_pasteur.fr
> Bioinformatique Structurale
> CNRS URA 2185
> Institut Pasteur
> 75724 Paris
> France
> tel: +33 1 45688546
> fax: +33 1 45688719
>
> 

-- 
Grace Brannigan
Assistant Professor
Center for Computational and Integrative Biology (CCIB) &
Department of Physics
Rutgers University, Camden, NJ
(856)225-6780
www.branniganlab.org