Re: AMBER: 5 Ligands and 1 Protein

From: Colby C <>
Date: Thu, 21 Jun 2007 16:45:46 -0500

I need help with the naming and order. Does the pdb with the protein and 5
ligands have to be in a certain format. I know that the 4th column has the
Name of the molecule. This is how my pdb is:


The 4th column in the 13,000 atom protein has the residue names. (HIS, MET,
ASN, GLU....) The 4th column in each of the ligands has the name

I am not what to do with the names and the order to load files, source FF,
and open prepins or frcmod.

thank you

On 6/21/07, David A. Case <> wrote:
> 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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Received on Sun Jun 24 2007 - 06:07:33 PDT
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