I'm confused... I just tested creating an OBMol with a PDB with ~32K atoms and
it worked.
I definitely remember reading discussion where Noel was mentioning a limit
(that at this point can't be 1k atoms) but I can't find it since Sourceforge
seems to be down for maintenance.
In any case, dealing with proteins using chains can be a good choice to
simplify the workflow (at least in my experience).
S
----
Stefano Forli, PhD
Staff Scientist
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: (858) 784-2055
fax: (858) 784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
________________________________________
From: Geoffrey Hutchison [geoff.hutchi...@gmail.com]
Sent: Tuesday, February 10, 2015 9:13 AM
To: Browning Nicholas John
Cc: Da Silva Perez Marta Andreia; openbabel-devel@lists.sourceforge.net
Subject: Re: [OpenBabel-Devel] Mol2 atom number restriction
I have used mol2 files with many thousands of atoms. Can you explain why you
think there's a restriction or send me an example file?
Thanks very much,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu<mailto:geo...@pitt.edu>
web: http://hutchison.chem.pitt.edu/
On Feb 10, 2015, at 10:13 AM, Browning Nicholas John
<nicholas.brown...@epfl.ch<mailto:nicholas.brown...@epfl.ch>> wrote:
Hi All,
It seems to me that there is a restriction on the number of atoms (~1000) OB
can handle when using mol2 file format. I know this is also true for SMILES and
InChI however this doesn't make much sense for mol2.
I currently do mutations/atom manipulations with large proteins with
non-standard residues, so its a requirement that I load molecules with formally
defined bonding. Loading with PDB leads to incorrect bonding when I attempt to
dump out after modifications.
Can anyone offer any solutions?
Nick
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now.
http://goparallel.sourceforge.net/_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net<mailto:OpenBabel-Devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
