AMBER Archive (2007)

Subject: Re: AMBER: 5 Ligands and 1 Protein

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 20 2007 - 18:46:23 CDT

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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