VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 22:57:32 CDT

Hi,
  You'll want to read through the NAMD tutorial section
about topology files, as it describes the purpose of patches
for the the terminal residues:
 http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node21.html

I don't know the answer regarding charged states, you'll have to ask
Jim Phillips about that, (jim_at_ks.uiuc.edu) as he wrote the psfgen.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 04, 2006 at 05:23:25PM -0400, Margaret Shun Cheung wrote:
> Dear VMD wizards,
>
> I would like to know what kind of charged states psfgen would generate
> from a standard pdb structure.
> Do I have to worry about adding charges at all?
> Also, when I read the psfgen user guide, it said psfgen will
> patch N-terminal and C-terminal atoms. What does "patch" means? Do these
> termini carry charges?
> Thank you.
> Sincerely,
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------ 

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