Re: AMBER: PDB files

From: David A. Case <>
Date: Mon, 30 Apr 2007 13:00:33 -0700

On Mon, Apr 30, 2007, Beale, John wrote:

> There is no naming information in the file for the ligand
> (e.g., there is no "H3, C5, N1 types of designations). There might be a
> large number of hydrogens, for instance, but none possesses a unique
> name. All of them are listed as "H".

> I have processed all of my ligand structures through antechamber and
> these files have the complete atom designations.

Take a ligand pdb file from antechamber, and manually insert it into the main
pdb file at the spot where the ligand belongs (removing what sybyl put there).
Be sure there is a TER card between the protein and the ligand.

...hope this helps....dac

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Received on Wed May 02 2007 - 06:07:20 PDT
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