Dear Users,
I am using openbabel to protonate molecules from sdf file.
Using obabel version 2.3.2, several molecules cannot be protonated.
Using the python binders pybel/openbabel, I noticed that the the problem is
related to the output of the structure as a new sdf file.
I.e.
1: load molecule
cpd = pybel.readfile("sdf", moli).next()
2: protonation
cpd.OBMol.AddHydrogens(False, pHcorr, pH)
3: save output
pybel.Outputfile("sdf",fname,overwrite=True)
The problem is never related to the step 1 or 2 (even changing the
protonation options) but at step 3, the code gets stuck.
The same problem happens when running openbabel from terminal
i.e.
obabel -isdf am0000000003.sdf -osdf -p 7.4
or obabel -isdf am0000000003.sdf -osdf -p
The issue takes place ONLY with some compounds and it is reproducible among
them (in attachment you can find an example), even if I couldn't find a
regular pattern.
The same compounds are correctly protonated using older versions of
openbabel (both 2.3.0 and 2.3.1, install from rpm packages available within
debian, ubuntu and centos). The version that gives problem is the 2.3.2,
compiled (without no apparent errors) on two different systems.
I was wondering if anyone experienced similar problems with 2.3.2 version
and if anyone has any suggestion about that. I was also wondering if someone
using the 2.3.2 version could try to protonate the attached file, to be sure
it is not my problem related to the compilation of the software.
Thanks to everybody in advance,
Luigi
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