Dear AMBERs,
I'm trying to get gaff parameters for a molecule of berenil following
the standard procedure from the antechamber tutorial. When I use bcc
charge model, the atomic types as well as the charges are recognized
wrongly (see am1bcc_berenil.mol2 attached): among other inconsistencies,
one of the ring is treated as a benzene ring, which is correct and
another is not. If I simply use openbabel with Gasteiger charges,
everything is recognized correctly (see babel_berenil.mol2 and
babel_berenil.pdb attached). The wrong assignments in antechamber are
independent of the geometry of the molecule (I tried several minimized
conformations). Are there any ways to fix this problem? Is there the way
to rewrite mol2 with Gasteiger charges into mol2 with AM1BCC charges
changing the type of atoms and bond accordingly?
If I try to use individual scripts within antechamber instead of
antechamber as the whole, I get probably something more proper
(probably_correct.ac) in .ac format. So assuming that the values in this
file are correct, how can I convert this file into a mol2 file? If I
could do this, then I probably have solved the problem by a stepwise
execution of the scripts from antechamber.
Thanks a lot in advance and cheers,
Sergey
--
Sergey Samsonov, PhD
Project Leader at Laboratory of Molecular Modeling,
Department of Theoretical Chemistry,
Faculty of Chemistry,
University of Gdansk
ul. Wita Stwosza 63
80-308 Gdańsk, Poland
phone: +48 58 523 5166
prot-gag.org
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Received on Thu Aug 16 2018 - 08:30:01 PDT
