Hi Stefano,
the problem with the PDBQT format is that connectivity is implicit and bond
order is lost.
If your atom coordinates are close to ideal (i.e., bond lengths are optimal,
non-distorted) you have a good chance of OB to be able to re-build the correct
bond order.
Although, there's been some discussion in the mailing list about similar
problems using PDB files as well.
My advice is to manually correct the issues, hoping you don't have too many
files to process.
Best,
S
--
Stefano Forli, PhD
Assistant Professor of Integrative
Structural and Computational Biology,
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: fo...@scripps.edu
http://www.scripps.edu/~forli/
________________________________________
From: Stefano Guglielmo [stefano.guglie...@unito.it]
Sent: Monday, January 04, 2016 4:12 PM
To: openbabel-discuss@lists.sourceforge.net
Subject: [Open Babel] azoxy
Dear opnebabel users,
I've made docking with autodock of some molecules containing an azoxy function;
I need to generate sdf file from pdbqt, but openbabel seems to manage the
molecules not so well as it adds hydrogens to the azoxy group.
Any suggestion about generating a correct sdf file?
Thanks a lot
--
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707678
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