VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Sep 07 2007 - 11:26:41 CDT

> Does VMD have this capability yet? An extension possibly?

You could try molefacture to do the task (although I haven't try it yet).

>
> To what extent can VMD be used to build and parameterize a new molecule (a
> new ligand for instance, in drug discovery)?
>

You can use the paratool plugin for such task. However, even with its
aid, the parametrization process can be quite tedious. Here's the
link: http://www.ks.uiuc.edu/Research/vmd/plugins/paratool/

Good luck! Michel

> Thanks,
>
> Arneh
>
>
>
> > No, Molden has a function to automatically build a whole peptide given
> > the sequence. It is very simple, is not like building other
> > structures, which would certainly be tedious.
> > Leandro.
> >
> >
> > On 4/22/06, dimka <newyorkdimka_at_gmail.com> wrote:
> >> Molden is great for adding/modifying small chemical groups. Building
> >> an 11-residue fragment will be very tedious. I'd use Modeler for
> >> rebuilding the fragment.
> >>
> >> -d
> >>
> >> On 4/22/06, Leandro Martínez <leandromartinez98_at_gmail.com> wrote:
> >> > Molden does that.
> >> > Leandro.
> >> >
> >> >
> >> >
> >> > -------------------------------------------
> >> > Leandro Martinez
> >> > Institute of Chemistry
> >> > State University of Campinas
> >> > http://www.ime.unicamp.br/~martinez/packmol
> >> > -------------------------------------------
> >> >
> >> > On 4/21/06, John Robinson <johnmrobinson_at_mac.com> wrote:
> >> > > Can anyone recommend free software that enables one build a peptide
> >> > > fragment into a pdb structure that has an 11 residue void.
> >> > >
> >> > > Thanks,
> >> > >
> >> > > --John
> >> > > --------------------------------------------
> >> > > John M. Robinson, M.D., Ph.D.
> >> > > mailto:johnmrobinson_at_mac.com
> >> > >
> >> > >
> >> > >
> >> >
> >> >
> >>
> >>
> >
>
>