Re: [AMBER] Antechamber ligand parametrization

From: Hannes Loeffler <>
Date: Tue, 16 Sep 2014 12:55:55 +0100

It is not quite clear what you are asking for, you say "hybridization"
in the context of some "cyclic" groups. Maybe you mean more
specifically the protonation state/tautomerism. In this case, my
recommendation would to read e.g. DOI:10.1007/s10822-010-9329-5 (one
chemoinformatician's point of view) and understand that this may be a
problem much more complicated than just throwing a file at an
algorithm. Chemists tend to be "sceptical" about such approaches. If
that is not the problem the software is still reliant on "reasonable"
input structures (you don't say how you got to those).


On Tue, 16 Sep 2014 15:14:59 +0400
James Starlight <> wrote:

> Dear Amber users!
> Using antechamber I need to parametrize broad set of the ligands,
> dock it with the receptors and proceed complexes for further md run.
> The problem on the first step: is due to all of those ligands are
> consisted of several bulk cyclic group so it's hard to determine
> hybridization of each C atom and compute precice number of hydrogens
> (I've tried to do it by chimera pymol and babel taking ligands
> stripped from any hydrogens as the input structures). Could someone
> suggest me some software(or alternatively combination of commands for
> above listed ones) to solve this issue?
> James
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Received on Tue Sep 16 2014 - 05:00:02 PDT
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