Yes, I confirmed by pubchem:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=45266541&loc=ec_rcs#Properties
And I just confirmed the imput mol2 structure (attached).
Thanks!
On Thu, Apr 14, 2011 at 12:51 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> Are you sure the total charge should be -4 ?
>
> I think it should be -3, but then again, my chemistry degree is OLD...
> a.
>
>
> On 4/14/11 6:46 PM, Yuan Yao wrote:
> > Thanks! dac,
> >
> > Yes, I have readed. and I even used the following ...
> >
> > ~$ antechamber -i coa_h_bbd_x.mol2 -fi mol2 -o coa_final.mol2 -fo mol2 -c
> > bcc -s 2 -nc -4 -j 1 -ek "qm_theory='AM1', grms_tol=0.0002,
> tight_p_conv=1,
> > scfconv=1.d-8, qmcharge=-4, itrmax=200, maxcyc=9999,"
> >
> > and I attached the sqm.out
> >
> >
> > On Thu, Apr 14, 2011 at 12:35 PM, David A Case<case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Thu, Apr 14, 2011, Yuan Yao wrote:
> >>>
> >>> I need to parameterize acetyl-coa in my MD. But antechamber does not
> work
> >>> since sqm can not converge.
> >>
> >> Have you read Note 6 in Section 4.2 of the Users' Manual?
> >>
> >> ...dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 14 2011 - 10:30:06 PDT
