AMBER Archive (2007)

Subject: Re: AMBER: 5 Ligands and 1 Protein

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 21 2007 - 00:02:20 CDT

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

Antechamber would be run for each ligand in turn. That is, you would run
antechamber 5 times, giving it a small pdb file each time.

After than, you would run LEaP once, giving it a pdb file with all the
coordinates (protein + 5 ligands).

The tutorials show how to handle a protein + 1 ligand. Be sure you understand
that first. Try your problem with just one of the 5 ligands, following what
the tutorial does. Then work on the harder problem.

...dac

>
> Sorry for the confusion but amber is super unclear.

If you can point to particular places in the documentation that confused you,
that might help in revisions.

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