ADL: prepare_ligand4py fails on quaternary nitrogen atoms
bennion1 at llnl.gov
Mon Dec 8 16:35:14 PST 2014
Thank you for the quick reply.
The work path I am following uses a pdb file containing all hydrogen atoms that has been subjected to energy minimization. prepare_ligand4.py -l somefile.pdb is then called. An error is given stating that only 6 of 23 atoms were written. So I explicitly select the quaternary nitrogen as root with -R 4 (the atom index).
This allows all but six atoms to be converted. These six atoms are a complete branch from the quaternary nitrogen atom.
Which method do want to me to send the file?
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] on behalf of Stefano Forli [forli at scripps.edu]
Sent: Monday, December 08, 2014 4:28 PM
To: autodock at scripps.edu
Subject: Re: ADL: prepare_ligand4py fails on quaternary nitrogen atoms
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
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tel: +1 (858)784-2055
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email: forli at scripps.edu
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