Dear Hoshin,
Several points I would like to underline:
- I think it is important you know that the Amber force fields
generally used by the community & available in the AMBER distribution
were all obtained using RESP charges. Historically, Amber force fields
use the Gaussian program for geometry optimization & MEP computation.
- Divcon, then(or before) Mopac & now sqm were/are sequentially used
to get AM1-BCC charges. Here, I am totally lost between these
possibilities and the choices made behind the approach.
- Moreover, AM1-BCC charges were originally parametrized to reproduce
QM MEP and the AM1-BCC charge model is used for its weak computational
cost & its simplicity. HF/6-31G* which is generally used in RESP
charge derivation costs nothing nowadays with the new computers and
RESP charges can now easily be derived using either Antechamber or
R.E.D..
- Finally, if you decide to use the R.E.D. Tools (or R.E.D. server)
the charges you are going to generate are _reproducible_ with an an
error of ~.0001 e. This presents many advantages; in particular, new
users can rigorously check if their approach is correct. Many examples
are available in R.E.DD.B. to check the data generated. Finally only
the R.E.D. Tools allow the generation of molecular fragments, and
handle multiple conformations & multiple molecules in charge
derivation. All these tools are available .
http://q4md-forcefieldtools.org.
regards, Francois
Quoting Alan <alanwilter.gmail.com>:
> 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
>>
>>
>> _______________________________________________
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>> 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<<
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>
>
F.-Y. Dupradeau
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Received on Fri May 14 2010 - 00:30:04 PDT
