It seems this bug came back a few times in the past:
https://sourceforge.net/p/openbabel/bugs/710/
S
On 06/19/2018 09:09 AM, Geoffrey Hutchison wrote:
We're not responsible for Autodock - you might want to contact them.
As far as small molecules getting large total charges, that's a bug - can you
give us an example and file it at:
https://github.com/openbabel/openbabel/issues
Thanks and best regards,
-Geoff
On Jun 14, 2018, at 8:44 AM, MichaelSmith <michaelsmith8...@gmail.com> wrote:
Hi,
According to the 2006 J Comput Chem paper describing Autodock 4, OpenBabel
was used to add hydrogens and assign Gasteiger charges to the protein and
ligands that were used as the training set to calibrate the force field. I
just want to ask whether the -p option in OB was used to do this (where it
allows the user to specify a pH so that it can attempt to calculate
protonation states). There has been a bug discovered in this usage of
OpenBabel where very large charges can get assigned to molecules. I have
seen one example of a small molecule being assigned a total charge of -9,
when it reality it contains a single ionizable group.Can someone please
comment on whether this might have had an impact on the accuracy of
Autodock's force field?
Please help.
I didn't find the right solution from the Internet.
References:-
http://mgl.scripps.edu/forum/viewtopic.php?f=9&t=1398
Thanks!
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Dept. of Integrative Structural
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