ADL: pdb_to_xyzr

Sargis Dallakyan sargis at
Sun Aug 19 21:21:07 PDT 2012


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Regarding converting  pdb files into xyzr. I have implemented OpenBabel widget in PyRx that should be able to handle this -

Please let me know if you have questions or need more information.


Sargis Dallakyan, Ph.D. - Research Programmer

Prof. Art Olson's Molecular Graphics Lab
Department of Molecular Biology
The Scripps Research Institute
10550 North Torrey Pines Road, MB5
La Jolla, California, USA  92037
Tel: (858) 784-2333


Automated Molecular Imaging
National Resource for Automated Molecular Microscopy
The Scripps Research Institute
10550 North Torrey Pines Rd. CB-112
La Jolla, California, USA  92037
Tel: (858) 784-9040
From: autodock-bounces at [autodock-bounces at] On Behalf Of Javier Rama Morales [jjramauy at]
Sent: Sunday, August 19, 2012 2:53 PM
To: autodock at
Subject: ADL: pdb_to_xyzr

Hello to everyone, I'am traing to convert some pdb files into xyzr but I
have several error menages like:
error, file 1CGN.pdb line 1187 residue  103 atom pattern ASP C was not
found in ./atmtypenumbers
and several more similar, I guess that I have to update the atmtypenumbers
file, but I do not know how, if someone can give me a lead of what to do
I'll be very grate full.
Javier Rama

José Javier Rama Morales.
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