Re: [AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files

From: Scott Brozell <>
Date: Tue, 2 May 2017 03:20:56 -0400


On Mon, May 01, 2017 at 03:09:32PM -0700, Niel Henriksen wrote:
> I haven't used acdoctor before, but now that it is bundled with
> antechamber, I'm seeing a possible bug with carboxylate functional groups.
> If I read in a structure from a PDB file, generate charges with AM1-BCC,
> and write to a Mol2 file, everything seems fine:
> $ antechamber -i but.pdb -fi pdb -o but.mol2 -fo mol2 -c bcc -nc -1
> ... blah blah ...
> acdoctor mode has completed checking the input file.
> Info: Total number of electrons: 48; net charge: -1
> Running: /usr/local/amber16gnu/bin/sqm -O -i -o sqm.out
> But then if I read in the subsequent Mol2 to convert to another file format
> or to even change the atom types, acdoctor gives a fatal error:
> $ antechamber -i but.mol2 -fi mol2 -o but.sybyl.mol2 -fo mol2 -at sybyl
> ... blah blah ...
> -- Check Weird Bonds --
> /usr/local/amber16gnu/bin/to_be_dispatched/antechamber: Fatal Error!
> Weird atomic valence (3) for atom (ID: 1, Name: C1).
> Possible open valence.
> The obvious workaround is to disable acdoctor with the '-dr n' flag, but it
> seems like acdoctor should be able to handle a carboxylate group .... so
> there might be a bug lurking in there somewhere. I've attached the file
> used above (but.pdb) to reproduce.

Thanks for the report; i'll investigate tomw.


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Received on Tue May 02 2017 - 00:30:07 PDT
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