AMBER Archive (2006)

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

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Tue Sep 26 2006 - 22:49:34 CDT

Dear Sir
   
  when we load a single peptoid residue in antechamber it appears in leap list but once we close leap and reopen it the residue loaded is missing in the list.
   
  With Regards
  Priya Anand

Junmei Wang <jwang_at_encysive.com> wrote:
  Besides Dave's comment, please bear in mind that the following message
is just for information, not a real error:

"The atom number exceeds the MAXATOM, reallocate memory"

Junmei

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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