Re: AMBER: Problem generating .prepin file in Antechamber

From: David A. Case <>
Date: Thu, 2 Aug 2007 13:53:03 -0700

On Thu, Aug 02, 2007, Lili Peng wrote:
> "The atom number exceeds the MAXATOM, reallocate memory

This should give you a clue. Antechamber is designed for single residues,
not for full proteins or polypeptides. Your pdb file has 35 glu residues,
where every atom has the same name and all atoms are listed as being in
residue "0".

You will need to make a pdb file for just a single residue, with unique atom
names. Then, antechamber can help you get parameters for that. Then, you
use LEaP to link the 35 residues together into a single macromolecule.

[If these residues really are glutamic acid, you don't need antechamber
at all: just use one of the standard amino acid libraries provided with

...good luck...dac

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Received on Sun Aug 05 2007 - 06:07:41 PDT
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