Hi,
I had a similar issue and my recollection is that it's a hardcoded limit in
OpenBabel. Not sure how feasible would be to remove or extend this limit, but
in the meantime I had to find workarounds to get the job done.
The best solution for me was to write a file parser to process a chain at the
time. So far it worked fairly well.
Writing a single Mol2 output is not feasible with this method, but you could
write a PDB by concatenating the single-chain outputs with minimum effort.
Hope this helps.
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: Browning Nicholas John [nicholas.brown...@epfl.ch]
Sent: Tuesday, February 10, 2015 7:13 AM
To: openbabel-devel@lists.sourceforge.net
Cc: Da Silva Perez Marta Andreia
Subject: [OpenBabel-Devel] Mol2 atom number restriction
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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