AMBER Archive (2008)

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

From: David A. Case (case_at_scripps.edu)
Date: Fri Jun 06 2008 - 13:59:52 CDT

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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