Hoshin,
One thing that hasn't been mentioned is that the carbohydrate RESP charges
(in Glycam) have been developed and tested for aqueous simulations. I'm
only mentioning this because sugar conformational preferences can be 'tuned'
through electrostatics. Have you already tested your charge models? If
not, then once you've developed 'optimized' structures it would be worth
trying several charge models (whether that's using ESP charges, varying RESP
weights or using something simplistic like Gasteiger charges) on a
well-characterized sugar in an ionic solvent to ensure the charges are
appropriate.
Matthew Tessier
mbt3911.uga.edu
matthew.tessier.gmail.com
Woods' Lab Room 1092
Complex Carbohydrate Research Center - University of Georgia
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Hoshin Amber
Sent: Thursday, May 13, 2010 3:51 AM
To: 'AMBER Mailing List'
Subject: RE: [AMBER] ESP VS AM1BCC
Dear Jason, Alan, and all amber user
I'm not using SQM or MOPAC. Is this program(?or command) in the amber-tool
package? Like antechamber? I've searched the manual to find how to use SQM
and MOPAC, but that is not mentioned. Now I'm using AMBER9. In this program,
in this program "DIVCON" seems to be used for optimization structure instead
of SQM and MOPAC.
Is it Ok to use DIVCON instead of SQM or MOPAC?
If yes, is it automatically applied, when I use antechamber? Please reply
with reference below.
If no, Could you tell me how to use SQN and MOPAC before running ANTECHAMBER
?
>antechamber -i tfo.mol2 -fi mol2 -o tfo.ac -fo ac -c bcc -nc -1 -s 2
Running: /usr/local/apps/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Running: /usr/local/apps/amber9/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 74; net charge: -1
Running: $AMBERHOME/exe/divcon
Running: /usr/local/apps/amber9/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p
/usr/local/apps/amber9/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /usr/local/apps/amber9/exe/atomtype -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
Thanks in advance
Hoshin Kim,
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Jason Swails
Sent: Wednesday, May 12, 2010 9:49 PM
To: AMBER Mailing List
Subject: Re: [AMBER] ESP VS AM1BCC
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
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
> >><http://www.bio.cam.ac.uk/%7Eawd28><<
> _______________________________________________
> 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
_______________________________________________
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 Wed May 12 2010 - 16:00:03 PDT
