On Wed, May 12, 2010 at 5:58 AM, Alan <alanwilter.gmail.com> wrote:
> 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
>
This is a good point. The gaussian structure used to find the charges from
should be minimized.
All the best,
Jason
>
> 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
> > >
> > >
> > >
> > > _______________________________________________
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> > > 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 <http://www.bio.cam.ac.uk/%7Eawd28><<
> _______________________________________________
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> 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
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Received on Wed May 12 2010 - 06:00:09 PDT
