HI Hoshin,
Divcon is just another option and doing almost the same thing that sqm/mopac
do. If I remember well, there will be a file divcon.pdb on the output of
your antechamber and this would be the optimised one. If not, I am sure that
in divcon.log there's the coords.
Nevertheless, check what Matthew suggested.
Alan
On Thu, May 13, 2010 at 08:51, Hoshin Amber <85hskim.gmail.com> wrote:
> 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
>
--
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 Thu May 13 2010 - 02:30:06 PDT
