[AMBER] Antechamber ligand parametrization

From: James Starlight <jmsstarlight.gmail.com>
Date: Tue, 16 Sep 2014 15:14:59 +0400

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?

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Received on Tue Sep 16 2014 - 04:30:02 PDT
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