Dear Richard,
Others might know more, but as a workaround you might try UCSF Chimera
in order
to do the PDB to MOL2 conversion.
Regards,
F.
On 09/07/2021 19:52, Richard Gillilan wrote:
Hello all,
I'm actually back to this list after nearly twenty years. Nice to see
this package is still actively maintained!
It will take me a while to get back up to speed, but my needs are the
same as they were back then when I published some docking work using
the code:
I use openbabel to convert pdb files to mol2 adding bond orders and
protonation states for proteins. My code then uses the bond orders to
assign forcefield parameters for simulation purposes.
I did a preliminary conversion of lysozyme: obabel -p 7.0 -ipdb
6lyz_no_wat.pdb -omol2 >! test.mol2
Seems like there are a number of incorrect bonds formed. I have a very
old note that openbabel often failed to assign carbonyl oxygens a
double bond. In principle, knowledge of the amino acid 3-letter code
should solve the bonding problems.
Anyone worked on this aspect of openbabel in the past?
Richard Gillilan
HP-Bio/BioSAXS
Cornell High Energy Synchrotron Source
Ithaca, NY
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