VMD-L Mailing List

From: NAMITA BHADRA (namitabhadra_at_gmail.com)
Date: Sun Sep 20 2009 - 08:50:18 CDT

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
>