VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 26 2007 - 02:10:24 CST

Hi,
  For detailed questions about paratool, you'll want to talk
to Jan Saam, the author of the plugin. There's also a fairly
lengthy document Jan has made available on the paratool plugin
documentation page which should help with the most basic
questions you may have. He may be able to answer other items that aren't
covered there.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 24, 2007 at 11:18:01PM +0100, Javaria Ahmed wrote:
> Hi
>
> My question is regarding paratool;
>
> Paratool accepts pdb file as input of base molecule, my molecule is an
> inorganic diatomic crystal. (I want to load a base molecule of lets say 14
> atoms)
>
> How will paratool parameterize a molecule without knowing atom connectivity
> (i.e psf file), that what is its crystal structure, how are atoms
> connected, which atoms are connected and which are not?
>
> And how can I edit such a structure in Molefacture.
>
> Regards
>
> javaria 

-- 
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/      Fax: 217-244-6078