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.
Dean
Dr. Dean Cuebas, Associate Professor of Chemistry
deancuebas.missouristate.edu, 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" <erkelly4572.gmail.com> 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
>ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
>Running: /home/erkelly/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
>ANTECHAMBER_AC.AC -p gaff
>
>Total number of electrons: 488; net charge: 0
>
>Running: /home/erkelly/amber11/bin/sqm -O -i sqm.in -o sqm.out
>Error: cannot run "/home/erkelly/amber11/bin/sqm -O -i sqm.in -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 - 13:30:03 PDT
