ADL: prepare_ligand4py fails on quaternary nitrogen atoms
forli at scripps.edu
Mon Dec 8 16:28:59 PST 2014
it would be helpful if you could provide an example of such molecules and a description of
what the specific issue is (e.g. unrecognized rotatable bonds, misplaced hydrogens, etc...).
Without a well-defined structure it is hard to help, but a general advice for peculiar
molecular structures is to add hydrogens using tools that are more sophisticated than
AutoDockTools (that's known to have problems with some nitrogen-containing structures),
then generate the PDBQT file with the scripts or the graphical interface.
On 12/08/2014 04:24 PM, Bennion, Brian wrote:
> I am wondering if there is a way to help prepare_ligand4.py recognize and properly prepare ligands for docking when they contain a quaternary nitrogen in which two bonds are part of a 6 member ring.
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Stefano Forli, PhD
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: forli at scripps.edu
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