VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu May 21 2009 - 12:48:40 CDT

On Thu, 2009-05-21 at 13:32 -0400, KIRTANA S wrote:
> If I use topotools plugin with scripts as suggested in your mail ,what
> should I replace for the index numbers . I am a first time user and

topotools uses VMD style, i.e. zero based indexing.

the package is completely independent from the file format (that is the
whole point of writing something like that within VMD). in fact, it was
started with the intent to write some generalized topology manipulation
tools for use with LAMMPS and HOOMD, which have different formats.

> non able to decide on it .Can you suggest an example if my psf file
> is :

try typing:

package require topotools
topo help

at the VMD command line prompt and see what you can figure out.

axel.

[...]

> I need to add the bond for Au and bond angles in the file .

> Thanks and regards
> kirtana
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.