RE: [AMBER-Developers] Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala

From: Andreas Svrcek-Seiler <>
Date: Wed, 11 Nov 2009 22:01:29 +0100 (CET)

Hi Ross,
> Just to be clear this is a very different issue than being able to use
> AmberTools 1.2. In v1.2 divcon is used for the charge calculations in
> Antechamber. In v1.3 it uses sqm so the code paths are completely different.
... I did not know this. Sorry I've raised a false alarm. The many
instances where valgrind complains about test-runs might have made me a
bit paranoid.
(And these valgrind warnings and the (putative) bugs behind them seem to
date back quite some time - so I thought this might have been a dormant

Anyway, I've seen something similar in
where the chamber exits with
At line 317 of file _molnt.f
Fortran runtime error: Array reference out of bounds for array
'atom_to_molecule_map', lower bound of dimension 1 exceeded (0 < 1)

when all runtime checks (I'm aware of) are turned on.
...might be another false alarm but it seems better to err on the side of


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Received on Wed Nov 11 2009 - 13:30:02 PST
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