VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jan 03 2008 - 15:38:31 CST

Hi Snoze,

when you start molefacture, a dialog box should initially pop up asking
for a selection. If you type in an atom selection corresponding to your
ligand of interest (eg, resname LIG) and then click start molefacture,
molefacture should start in a way that allows you to edit your ligand.

Please let me know if you still have trouble.

Peter

snoze pa wrote:
> 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
> <mailto: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 <mailto: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 <mailto: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
>
>