VMD-L Mailing List

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Jan 03 2008 - 15:30:40 CST

Thanks for your reply. I checked following website

http://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/

but unable to get any clue how to use it. When I am loading a ligand
molecule in vmd and using the GUI option of molefacture, the molecule get
disappear from the main window. All i have is black gui where I don't know
how to add hydrogen. There is no atom no or name in molefacture screen. I
try to use PHE residue to do so but still I am unable to see the PHE
residue/no/name etc in molefacture screen? I used autopsf and it is fine,
but I want to prepare molecule for docking studies.

Any help(tutorial) using standard molecule in molefacture will be of great
help.

thanks in advance
s

On Jan 3, 2008 2:26 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> Depending on what you mean there are two straightforward methods
> for doing this. You can automatically add hydrogens missing from a PDB
> using the autopsf plugin, which invokes psfgen which does this. If you
> want to manually modify a residue, try the molefacture plugin.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jan 03, 2008 at 02:08:31PM -0600, snoze pa wrote:
> > Dear Vmd users,
> > Is it possible in vmd to add hydrogen atom to protein or ligand? any
> help
> > thanks in advance and happy new year
> > s
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>