AMBER Archive (2007)

Subject: Re: AMBER: 5 Ligands and 1 Protein

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 20 2007 - 19:16:27 CDT

On Wed, Jun 20, 2007, Colby C wrote:

> 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.

No: you need one pdb file (provided to you by autodock) for use in the loadPdb
command in LEaP.

> I thought I
> needed to source the gaff for the ligand and the ff03 for the protein.

This is correct. After you do that, use the loadPdb command to get the
coordinates for the ligands (and the protein).

If this is too abstract, you'll have to post what LEaP commands you actually
used, and what happened. Then, maybe people can offer advice.

...dac

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