Thanks,
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?
David
On Tue, Jul 19, 2011 at 5:58 AM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> If you are talking about the minimization of the ligand in antechamber, you
> *should* expect it to change conformation, basically because its in a
> different environment than it had in the complex. However, the parameters
> generated by antechamber are just as valid. You can load those parameters,
> but use the PDB coordinates for the ligand.
>
> Gustavo.
> --
> Sent from my iPad.
>
> On 19/07/2011, at 01:54, David Cantu <cantudav.amber.gmail.com> wrote:
>
> > Dear Amber Users and Developers:
> >
> > I have a general question about placing a ligand (or cofactor) in the
> > correct position and conformation inside an enzyme's active site.
> >
> > Suppose you have a ligand (LIG) crystallized in an enzyme. You take LIG's
> > coordinates, add hydrgens, run it throough antechamber, make the mol2 and
> > frcmod files. But during minimizations its conformation was changed.
> >
> > What I want to do is keep the crystallized conformation of LIG (not the
> > minimized in the mol2), plus hydrogens. What needs to be done in Leap to
> > load LIG in its crystallized conformation, but use the parameters derived
> > from antechamber for GAFF?
> >
> > Thank you,
> >
> > David
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 19 2011 - 08:00:02 PDT
