Re: [AMBER] Antechamber trouble with COA-acyl chain

From: Erin Kelly <>
Date: Tue, 12 Jul 2011 11:19:24 -0500

Hello again,

I'd like to add a little to this question: has anyone else dealt with COA in
the past? How did you treat the double bonds in the ring structure? I'm
also a bit confused on how to deal with the protonation state of the
phosphorous atoms. We're concerned that these charges may be part of the
problem we're running into.


On Tue, Jul 12, 2011 at 9:59 AM, Erin Kelly <> wrote:

> Hello all,
> I've been trying to produce a mol2 file from a pdb generated using ChemDraw
> because 'reduce' would not add hydrogens to an unrecognized part of my
> ligand. The ligand is a COA with a 10 carbon acyl chain. Both COA and the
> acyl chain have gone through antechamber with no problems on their own, but
> when I put them together the run fails. I notice this because the sqm.out
> file populates itself immediately but gets stuck on atom 101. When I cancel
> the run I recieve an error message:
> *Running: /home/erkelly/amber11/bin/bondtype -j full -i
> Running: /home/erkelly/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> Total number of electrons: 488; net charge: 0
> Running: /home/erkelly/amber11/bin/sqm -O -i -o sqm.out
> Error: cannot run "/home/erkelly/amber11/bin/sqm -O -i -o sqm.out"
> of bcc() in charge.c properly, exit
> *
> I've also attached the sqm.out file for reference.
> I've tried to save the molecule directly to mol2 from ChemDraw but this
> fails in parmchk because it seems to lose all bond information.
> Any advice would be greatly appreciated.
> Thank you,
> Erin Kelly
> Iowa State University
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Received on Tue Jul 12 2011 - 09:30:02 PDT
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