VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 20 2004 - 15:06:59 CDT

Hi,
  If you build a complete structure using psfgen with the "guesscoord"
command if they are in the topology file. The psfgen documentation is
available here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/

There's a more complete tutorial on structure building here:
http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/02-namd-tutorial/namd-tutorial-html/node6.html

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 20, 2004 at 09:22:32AM -0700, chandran karunakaran wrote:
> Hi,
>
> I need to add H atoms to my protein
> pdb file to calculate NOE (NMR) simulation.
> Does any body know or have script file
> to convert pdb with hydrogen atoms.
>
> With thanks
>
> C.Karunakaran, PhD
> Biophysics department
> Medical college of wisconsin
> Milwaukee, WI-53226.
>
>
>
>
>
>
>
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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