AMBER Archive (2007)

Subject: Re: AMBER: 5 Ligands and 1 Protein

From: Colby C (colbychiauzzi_at_gmail.com)
Date: Thu Jun 21 2007 - 16:45:46 CDT

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:

Protein
TER
ligand1
TER
ligand2
TER
ligand3
TER
ligand4
TER
ligand5
TER
END

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
MO1,MO2.....MO5

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 <case_at_scripps.edu> 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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