Thanks again!
On Tue, Jul 19, 2011 at 11:19 AM, Gustavo Seabra
<gustavo.seabra.gmail.com>wrote:
> On Tue, Jul 19, 2011 at 12:40 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
> > On Tue, Jul 19, 2011, David Cantu wrote:
> >>
> >> Yes this is what I meant. In antechamber, sqm will optimize (minimize)
> the
> >> structure and change the conformation. This gives me a mol2 and from
> that
> >> the frcmod file.
> >>
> >> If I want to use the original pdb coordinates as my starting point, do I
> >> load the mol2? How in XLeap do I load original pdb coordinates, but keep
> >> mol2 and frcmod parameters?
> >>
> >
> > What Gusatvo (tried to) say:
> >
> >> > You can load those parameters, but use the PDB coordinates for the
> ligand.
> >
> > Use loadmol2 and loadamberparams to get the topology and parameters
> loaded.
> >
> > Then say something like this:
> >
> > x = loadPdb filename.pdb
> >
> > where "filename.pdb" has the coordinates of both the ligand and the
> receptor;
> > (or just the ligand if there is no receptor). Then "saveamberparm x
> ...."
> > will give you coordinates that came from the pdb file.
> >
> > ....dac
>
> Yep, thats what I meant. :-)
>
> Thanks!
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7417
>
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Received on Tue Jul 19 2011 - 10:00:02 PDT
