Are you using SQM or MOPAC?
Anyway, when using antechamber, the sqm/mopac will optimise the structure
and then calculate the charges although this "optimised" structure existed
only temporally. You still can try to recover it by getting the coords in
the mopac.out/sqm.out file.
I mention this because I don't know if you did optimise your mol with
gaussian and how much difference it would make.
Another suggestion is to used R.E.D.
http://q4md-forcefieldtools.org/RED/
Alan
On Tue, May 11, 2010 at 21:43, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, May 12, 2010 at 3:12 AM, Hoshin Amber <85hskim.gmail.com> wrote:
>
> > Dear, Amber user
> >
> > I'm trying to do dynamics of sugar(glucose, fructose, sucrose) solvation
> in
> > ionic liquids.
> > Before using ionic liquids structure to make solvent box, I ran
> > antechamber(Am1-bcc).
> > But some papers regarding my experiment have used gaussian03 for
> optimizing
> > their structure and then use antechamber(RESP, or ESP).
> >
> > Nevertheless I used same molecule(same structure), the charge value using
> > AM1BCC is different from using Gaussian-RESP(or ESP)
> > (For example, N2 on the imidazolium ring using AM1BCC and RESP
> > respectively,
> > : -0.017 / 0.19)
> >
> > Why there are great difference between AM1BCC and RESP? Which one is
> > precise
> > value of charge? Using AM1BCC directly. Or using Gaussian-ESP?
> >
> > (P.S Ionic liquids are the liquid that are composed of only ion pair.
> They
> > are not standard solvent in AMBER force field. One of ionic liquids which
> > I'm trying to use is EmimTfO(1-ethyl-3methylimidazolium
> > Trifluoromethylsulfonate) In case of Emim TfO, Emim is cation(+1), and
> TfO
> > is anion(-1))
> >
>
> I would use the Gaussian RESP if you've already done that calculation, as
> that's how the rest of the amber charges are derived (RESP/HF 6-31G*).
> AM1BCC should be sufficient for many applications, but I'd say RESP would
> be
> the better option to use. They shouldn't differ too much though...
> However, if I had both I'd use RESP (assuming it was done properly).
>
> Others may chime in with their comments and/or more professional opinions.
>
> All the best,
> Jason
>
>
> > Finally, I'm the beginner of Amber and Molecular Dynamics. Explain in
> > detail
> > please.
> >
> > Thank you for your help in advance.
> >
> > Regards,
> >
> > Hoshin Kim
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 12 2010 - 03:00:03 PDT
