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

From: Dean Cuebas <>
Date: Tue, 12 Jul 2011 15:04:04 -0500

The biggest problem is that your net charge should not be zero.

CoA has a net charge of -3.

If you need more help, let me know.

Dr. Dean Cuebas, Associate Professor of Chemistry, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

On 7/12/11 9:59 AM, "Erin Kelly" <> wrote:

>Hello all,
>I've been trying to produce a mol2 file from a pdb generated using
>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
>acyl chain have gone through antechamber with no problems on their own,
>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
>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"
>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 - 13:30:03 PDT
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