[AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber

From: Miroslav Suruzhon <ms2m18.soton.ac.uk>
Date: Thu, 10 Oct 2019 15:41:57 +0000


I have had some issues with antechamber when trying to read a PDB file
into it. This is only true for files generated by Open Babel 3.0 and not
earlier versions. I think the issue is that the new Open Babel writes
CONECT records with repeated indices for double and triple bonds, as
opposed to the previous Open Babel version which writes the indices only
once,, irrespective of the bond order. Conversely, antechamber has no
problem in handling files without any CONECT records either. Is this
intended behaviour? It would be very helpful if antechamber could at
least ignore CONECT records it cannot read because it doesn't seem to
require them in the first place. I have attached some files which prove
my point. The antechamber command I used for each one of these was:

antechamber -i {NAME}.pdb -fi pdb -o {NAME}.mol2 -fo mol2 -c bcc -at
gaff2 -s 2 -nc -1

Thank you for your help.

Kind regards,


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Received on Thu Oct 10 2019 - 09:00:03 PDT
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