Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber

From: Elvis Martis <>
Date: Thu, 10 Oct 2019 21:23:44 +0530

Since CONECT are redundant for antechamber, it is best to delete them.
Best Regards

On Thu, 10 Oct 2019 at 21:12, Miroslav Suruzhon <> wrote:

> Hello,
> 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,
> Miroslav
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Received on Thu Oct 10 2019 - 09:00:03 PDT
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