AMBER Archive (2008)

Subject: Re: AMBER: Problems simulating a protein-ligand complex

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Fri Jun 06 2008 - 17:16:29 CDT

Thank you, David.

With hydrogens added in another application, the antechamber part
worked.

But another issue appears when I combine the protein structure with the
antechamber output in xleap. The ligand is loaded as a prepin file,
followed by its frcmod with missing parameters. Then I load the pdb file
of the protein and use complex = combine { protein GNP }, where GNP is
the name of the residue assigned to the ligand. However, the ligand ends
up being shifted in space far from the protein, even though the initial
coordinates corresponded to the complex.. I assume that it's the result
of the intermediate operations.. but is there a way to combine the two
entities into the original complex?

Thanks for any advice

Sasha

On Fri, 2008-06-06 at 11:59 -0700, David A. Case wrote:

> On Fri, Jun 06, 2008, Sasha Buzko wrote:
> >
> > The structure has correct connectivity and came directly from a PDB
> > file. Since the ligand PDB file is not that large, I'm pasting it below.
> > Thank you for any suggestions.
>
> You don't have any hydrogen atoms in your input structure. Antechamber
> doesn't know how to add hydrogens...you need to draw them in by hand, or
> use some other model building program to add all of the hydrogens.
>
> ...hope this helps...dac
>
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