Hi Stefano,
I might suggest trying VS module in oddt (https://github.com/oddt/oddt)
which is based on Pybel (DISCLAIMER: I'm the author of oddt). To overcome
the connectivity problem it just copy the coordinates of docked
conformationson the input molecules. This way you should retain the
connectivity.[
https://github.com/oddt/oddt/blob/master/oddt/docking/AutodockVina.py#L199]
Sample docking pipeline is below. Note that comments (which allow you to
save scores) in mol2 files are available in development version of
OpenBabel. If you use stable, then use SDF.
from oddt.virtualscreening import virtualscreening as vs
# Initiate virtual screening pipeline using 8 CPUs
pipeline = vs(n_cpu=8)
# Load ligands from a mol2 file
pipeline.load_ligands('mol2', 'ampc/actives_final.mol2.gz')
# Dock entire library to receptor, autocenter docking box on ligand
pipeline.dock('autodock_vina', 'ampc/receptor.pdbqt',
'ampc/crystal_ligand.mol2')
# Write docked ligands conformations to a file (including scores)
pipeline.write('mol2', 'ampc_docked.mol2', overwrite=True, opt={'c':None})
The arguments for dock method:
http://oddt.readthedocs.org/en/latest/rst/oddt.docking.html#module-oddt.docking.AutodockVina
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-01-05 12:14 GMT+01:00 Stefano Forli <fo...@scripps.edu>:
> 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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