VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 17 2006 - 16:33:52 CST

Hi,
  You'll want to read the psfgen User's Guide and try
using the 'readpsf' command (without using intervening 'resetpsf' calls)
to merge your structures:
  http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/

You can use various existing psfgen scripts out there in
tutorials as a starting point, e.g.:
  http://mccammon.ucsd.edu/~rlaw/combine.tcl.htm

  John Stone
  vmd2ks.uiuc.edu

On Wed, Nov 15, 2006 at 11:06:06AM -0800, CSM USP wrote:
> Dear All,
> I am trying to run SMD using NAMD for cox-2
> inhibitors. I used VMD to convert pdb into psf. Now i
> have three psf files(one for protein, one for
> inhibitor and one for water). My questions:
> 1. Can i append all the three PSF files into one big
> PSF?
> 2. How can i generate the CRD files for co-ordinates?
> I would be grateful for any help,
> Thanks
> Kumar
>
>
>
>
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-- 
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