AMBER Archive (2007)

Subject: Re: AMBER: 5 Ligands and 1 Protein

From: Colby C (colbychiauzzi_at_gmail.com)
Date: Wed Jun 20 2007 - 21:01:40 CDT

Thank you!!

Autodock gives the best ligand conformations. For my protein I have to run
Autodock 5 different times to get the best ligands. (I think?) But I can
easily combine the protein and 5 ligands into one pdb.

I am really uncertain when I would run antechamber.

Sorry for the confusion but amber is super unclear.

thank you.

On 6/20/07, David A. Case <case_at_scripps.edu> wrote:
>
> 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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