ADL: pdb_to_xyzr

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


Greetings,

First some administrative notes. Because of a recent spam posts we have turned default_member_moderation flag on, which means that member postings are held for moderation. I do clear this flag for all members posting relevant contexts.  Please visit the following site for more information about GNU Mailman - http://www.gnu.org/software/mailman/mailman-admin/node22.html

Regarding converting  pdb files into xyzr. I have implemented OpenBabel widget in PyRx that should be able to handle this - http://www.youtube.com/watch?v=niw6gHDLfO4

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

Sincerely,
Sargis


--
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
http://mgltools.scripps.edu/Members/sargis

and

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
http://ami.scripps.edu/redmine/users/105
________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of Javier Rama Morales [jjramauy at gmail.com]
Sent: Sunday, August 19, 2012 2:53 PM
To: autodock at scripps.edu
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.
Cheres
Javier Rama

--
José Javier Rama Morales.
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



More information about the autodock mailing list