I used autodock prior to this; I know where the ligands dock. So you are
saying that I just need one pdb file to be used in antechamber. I thought I
needed to source the gaff for the ligand and the ff03 for the protein. One
of the tutorials prepared prepin files files for the ligand and the
protein. I am not sure of the correct way to prepare for SANDER.
thanks
On 6/20/07, David A. Case <case.scripps.edu> wrote:
>
> On Wed, Jun 20, 2007, Colby C wrote:
>
> > I am trying to prepare files for SANDER to run energy minimization of a
> > large protein with 5 ligands in 5 separate binding sites. We ran
> > antechamber with each of the 5 ligands and it made the 5 prepin files.
> > These files don't seem to have any missing parameters after running
> > parmchck. We are not sure how to combine these ligands with the large
> > protein.
>
> You presumably need to use loadPdb to load a pdb file that has the
> coordinates
> for the protein plus all of the ligands. If you don't know where the
> ligands
> bind, you are facing a "docking" problem that needs software beyond Amber.
> (You might consider Dock or Autodock, for example).
>
> ...hope this hleps....dac
>
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Received on Sun Jun 24 2007 - 06:07:18 PDT
