VMD-L Mailing List

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Jan 03 2008 - 15:53:31 CST

Thanks a lot peter. It was a great help.its working now

On Jan 3, 2008 3:38 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:

> 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
> >
> >
>