VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Sun Sep 20 2009 - 12:04:52 CDT

I assume you are using charmm force field.
I remember, there was a patch for deprotonated CYS called CYSD.

eddi

On Sep 20, 2009, at 3:50 PM, NAMITA BHADRA wrote:

> Hi,
> Thanks for reply. I am going through the Topology file
> tutorial.
> But now I create my PSF file through Auto-psf plug-in and the
> charge on the sulpher atom has been modified to -1.00 and I have
> decided to use this PSF file at the time of MD run. But there is a
> doubt in my mind that the hydrogen on SG atom is still present in
> the modified PSF file.
> Now my question is that may I use this modified PSF file for MD run?
> Please help.
>
> Thanks.
>
> Namita.
>
>
>
> On Thu, Sep 10, 2009 at 9:34 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
>

=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================