Re: AMBER: antechamber fails with large molecules

From: Francesco Pietra <>
Date: Thu, 1 Nov 2007 01:29:26 -0700 (PDT)

You may remeber that I tried unsuccessfully to get the partial charges with
Antechamber in Amber9 for a 500-atoms non-repetitive molecule. Prof Case, and
others, suggested, however, that, even if calculated, the partial charges would
be unreliable for such a large residue.

Is the new code intended to solve this question too?

At any event, do you plan to make the new code available? An when? I have
frequently problems of large ligands.


francesco pietra

--- Junmei Wang <> wrote:

> Could you send me the file? I have modified the respgen.c code a little bit
> to handle large molecules, but it is not in amber9.
> Best
> Junmei
> Dear amber users:
> 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
> resp() of charge.c properly, exit”.
> Could someone give me any idea about how to solve this
> type of problems?
> Thanks in advance,
> Vānia Calisto
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Received on Sun Nov 04 2007 - 06:07:21 PST
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