Re: AMBER: antechamber fails with large molecules

From: FyD <>
Date: Wed, 31 Oct 2007 15:02:36 +0100


> I am trying fit RESP charges with antechamber to a large organic
> molecule (342 atoms) with the command:
> antechamber –i biscalix.log –fi gout –o biscalix_resp.mol2 -fo mol2 –c resp
> This fitting process failed with the following errors:
> “The number of the path atoms exceeds MAXPATHATOMNUM(1900000) for
> atom[148],extend the size and reallocate the memory automatically
> reallocate memory for pathscore[148] failed
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Amber 9 RESP
> Error: cannot run "resp -O -i ANTECHAMBER_RESP1.IN -o
> ANTECHAMBER_RESP1.OUT -e ANTECHAMBER.ESP -t qout" in resp() of
> charge.c properly, exit”.

Personnally, I would avoid running such a huge job...
Do you control the molecular conformation you selected ?
What are the criteria for selecting this particular conformation ?
Is it just based on a guess originating from the building in a graphic
interface ?

Instead, I would split the big molecule into elementary fragments...

If antechamber needs to be recompiled when you are above a atom
number, the same will append with RESP. See
In the introduction, it is written:
RESP was recompiled using qtol = 0.1d-5, maxq = 5000, maxlgr = 500 and
maxmol = 200

regards, Francois

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Received on Sun Nov 04 2007 - 06:07:09 PST
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