We also tried it with a -nc -3, however, sqm did not run, due to the
followig error in the sqm.out file:
QMMM: System specified with odd number of electrons ( 311)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
calculatio
Have you worked with CoA before? We would appreciate any advice you might
have.
Thank you,
Erin
On Tue, Jul 12, 2011 at 3:04 PM, Dean Cuebas
<deancuebas.missouristate.edu>wrote:
> 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 - 13:30:05 PDT
