VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 10 2009 - 11:04:05 CDT

Hi,
  PSF building isn't really my area of expertise, but if you need to make a
non-standard residue, you'll probably find it helpful to read the basic
NAMD tutorial (which also covers the basic use of psfgen),
and the topology file tutorial:
  http://www.ks.uiuc.edu/Training/Tutorials/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 09, 2009 at 09:31:53AM +0530, NAMITA BHADRA wrote:
> Hi All,
>
>
>
> I am new in VMD.I want to create a PSF file of my protein
> having one cysteine residue as thiolate anion (want to delete the gamma
> hydrogen on sulpher atom) and one histidine as HSP state (keeping others
> as HSD state). How can I do these? Is it possible through autopsf plug-in?
> Please help me.
>
>
>
> Thanks in advance.
>
>
>
> Namita. 

-- 
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