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: [email protected]
http://www.scripps.edu/~forli/
________________________________________
From: Geoffrey Hutchison [[email protected]]
Sent: Tuesday, February 10, 2015 9:13 AM
To: Browning Nicholas John
Cc: Da Silva Perez Marta Andreia; [email protected]
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: [email protected]<mailto:[email protected]>
web: http://hutchison.chem.pitt.edu/
On Feb 10, 2015, at 10:13 AM, Browning Nicholas John
<[email protected]<mailto:[email protected]>> 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
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