AMBER Archive (2006)

Subject: Re: AMBER: Amber8: problem related to antechamber

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 22 2006 - 09:52:35 CDT

On Fri, Sep 22, 2006, priya priya wrote:
>
> I have a peptoid sequence (in peptoids the amino acid
> side chain is attached to the nitrogen instaed of
> carbon wrt proteins) of about 12-15 residues.
>
> I cannot load this molecule in antechamber.It says
> "The atom number exceeds the MAXATOM, reallocate
> memory".

Antechamber is designed to work with single residues at a time. You should
use it to create a unit for each peptoid residue you have, then use LEaP to
link them together into a polymer in the same way you would for a regular
protein.

...good luck...dac

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