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From: FyD <fyd.q4md-forcefieldtools.org>

Date: Fri, 27 Jun 2008 11:07:45 +0200

Quoting Junmei Wang <junmwang.gmail.com>:

*> Hopefully, AM1-BCC can remedy some flaw of Milliken charges, since it is
*

*> parameterized to mimic HF/6-31G* resp charges. It seems to me that am1-bcc
*

*> does not do a good job for some kinds of molecules, such as sulfonamides and
*

*> phosphates, more parameterization is needed for them.
*

Once again, I do not think 'simplicity' is the answer in a _general_

strategy for charge derivation/general force field for biomolecules.

Proposing a general/"on the fly" strategy based on some

parametrisation (am1-bcc) to reproduce a sophisticated charge

derivation (RESP with multiple conformations for instance) is in

contradiction with the rescent force fields. How can a parametrized

model reproduce something that is handled/understood/controlled with a

lot of ... difficulties ?

Indeed, RESP charges present many pitfalls; a parametrized model to

'mimic' RESP charges might be usefull for simple cases, but I do not

think it can be proposed as a general strategy. However, this is

clearly a convenient "black box" for new users.

In the Kollman group strategy, _the_ RESP charge model is the basis of

the strength of AMBER force fields. Rescent AMBER, GLYCAM, CHARMM

force fields use even more sophisticated/modified 'RESP' charge

derivation (high basis set, complex multi-conformation fitting

approach etc).

Once again, I do not understand how a parametrized model can reproduce

another complex model that is controlled with a lot of difficulties.

regards, Francois

*> On Thu, Jun 26, 2008 at 3:53 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
*

*>
*

*>> Quoting Junmei Wang <junmwang.gmail.com>:
*

*>>
*

*>> It is true that partial charges should depend on the environment. As a
*

*>>> matter of fact, different HF/6-31G* RESP charges are produced for
*

*>>> different
*

*>>> conformations (of course not significant different). However, in MM
*

*>>> calculations using an additive force field, only one set of charges is
*

*>>> used.
*

*>>> This set of charges should be "general" and "good" for all the
*

*>>> conformations
*

*>>> sampled by MD or minimization.
*

*>>>
*

*>>> How to generate such kind of charge? In AMBER, for standard aminio acid
*

*>>> and
*

*>>> nucleic acid residues, the charges were derived with RESP using multiple
*

*>>> conformations. Since Mulliken charges are less conformation dependent, one
*

*>>> may get such kind of "general" charges using only one conformation. From
*

*>>> this aspect, we say it is an advantage.
*

*>>>
*

*>>
*

*>> and for sure, it is also more simple to get Mulliken charges !
*

*>>
*

*>> However, from other aspects Mulliken charges were strongly criticized...
*

*>> Thus, it is a reason why many rescent force fields (AMBER, GLYCAM; even
*

*>> CHARMM !) use 'RESP' charges (and even quite sophisticated RESP charge
*

*>> derivation) or charges calculated based on molecular electrostatic
*

*>> potential(s); _NOT_ Mulliken charges.
*

*>>
*

*>> I am not sure 'simplicity' is the answer here...
*

*>>
*

*>> regards, Francois
*

*>>
*

*>>
*

*>>
*

*>> On Thu, Jun 26, 2008 at 12:29 PM, Francesco Pietra <chiendarret.gmail.com
*

*>>> >
*

*>>> wrote:
*

*>>>
*

*>>> On Thu, Jun 26, 2008 at 4:33 PM, Junmei Wang <junmwang.gmail.com> wrote:
*

*>>>> > Hi,
*

*>>>> > The bcc parameters are same and the final am1-bcc charges depend on
*

*>>>> which
*

*>>>> > am1 package to be used. However, I don't think the difference of
*

*>>>> charges
*

*>>>> of
*

*>>>> > Cl- is that significant. One advantage of am1-bcc over resp is that it
*

*>>>> is
*

*>>>> > less variant for different conformations since am1-mulliken charges are
*

*>>>> > pretty conformation independent.
*

*>>>>
*

*>>>> That lesser dependence of partial charges from the conformational
*

*>>>> status (if this is what you really meant) is interesting. However - as
*

*>>>> a devil's advocate - is that really an advantage? I wish you reassure
*

*>>>> me that it is an advantage. I always thought that it is normal for the
*

*>>>> partial charges to depend on the environment, be that also the
*

*>>>> conformational status itself. We are in the hot season, may be I can't
*

*>>>> rightly grasp what you wrote. Presently, I see that independence from
*

*>>>> the conformation as illusory, thus a disadvantage Sincerely, however,
*

*>>>> I hope I am wrong.
*

*>>>>
*

*>>>> francesco pietra
*

*>>>>
*

*>>>> >I think bcc parameters were derived using
*

*>>>> > the mopac package.
*

*>>>> >
*

*>>>> > Best
*

*>>>> >
*

*>>>> > Junmei
*

*>>>> >
*

*>>>> >
*

*>>>> > On Thu, Jun 26, 2008 at 1:21 AM, Dong Xu <d1xu.ucsd.edu> wrote:
*

*>>>> >>
*

*>>>> >> Hi Junmei,
*

*>>>> >>
*

*>>>> >> Thanks for your response. I installed ambertools and tested am1-bcc
*

*>>>> with
*

*>>>> >> mopac6. When comparing the output files of am1-bcc charge calculations
*

*>>>> from
*

*>>>> >> divcon and mopac for the same molecule, it seems they came to
*

*>>>> different
*

*>>>> >> optimized geometries and final electronic energies: -34543.95016086 EV
*

*>>>> >> (divcon) and -34945.38044 EV (mopac). The charges are thus different
*

*>>>> as
*

*>>>> >> well, e.g. a Cl atom has -0.00595 (divcon) and 0.012900 (mopac). So my
*

*>>>> >> questions are, How to reduce this type of variations in am1-bcc charge
*

*>>>> >> calculation and how much effect does it have on the protein-ligand
*

*>>>> >> electrostatic interaction energy estimation?
*

*>>>> >>
*

*>>>> >> Thanks,
*

*>>>> >>
*

*>>>> >> -DX
*

*>>>> >>
*

*>>>> >> On Wed, Jun 25, 2008 at 3:44 PM, Junmei Wang <junmwang.gmail.com>
*

*>>>> wrote:
*

*>>>> >>>
*

*>>>> >>> I would like to recommend you to use antechamber in AmberTools.
*

*>>>> Mopac6
*

*>>>> is
*

*>>>> >>> included in the package and you simply specify "-c bcc" to calculate
*

*>>>> am1-bcc
*

*>>>> >>> charges. For example antechamber -fi mol2 -fo mol2 -i input.mol2 -o
*

*>>>> >>> output.mol2 -c bcc
*

*>>>> >>>
*

*>>>> >>> Best
*

*>>>> >>>
*

*>>>> >>> Junmei
*

*>>>> >>>
*

*>>>> >>> On Wed, Jun 25, 2008 at 5:09 PM, Dong Xu <d1xu.ucsd.edu> wrote:
*

*>>>> >>>>
*

*>>>> >>>> Hi,
*

*>>>> >>>>
*

*>>>> >>>> I downloaded and compiled antechamber-1.27 and noticed that divcon
*

*>>>> is
*

*>>>> >>>> replaced by mopac6. Could anyone let me know the procedure and
*

*>>>> command
*

*>>>> to
*

*>>>> >>>> calculate am1-bcc charges using antechamber and mopac?
*

*>>>> >>>>
*

*>>>> >>>> Thanks,
*

*>>>> >>>>
*

*>>>> >>>> -DX
*

*>>>>
*

*>>>
*

*>>
*

*>> -----------------------------------------------------------------------
*

*>> The AMBER Mail Reflector
*

*>> To post, send mail to amber.scripps.edu
*

*>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
*

*>> to majordomo.scripps.edu
*

*>>
*

*>
*

F.-Y. Dupradeau

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Received on Sun Jun 29 2008 - 06:07:42 PDT

Date: Fri, 27 Jun 2008 11:07:45 +0200

Quoting Junmei Wang <junmwang.gmail.com>:

Once again, I do not think 'simplicity' is the answer in a _general_

strategy for charge derivation/general force field for biomolecules.

Proposing a general/"on the fly" strategy based on some

parametrisation (am1-bcc) to reproduce a sophisticated charge

derivation (RESP with multiple conformations for instance) is in

contradiction with the rescent force fields. How can a parametrized

model reproduce something that is handled/understood/controlled with a

lot of ... difficulties ?

Indeed, RESP charges present many pitfalls; a parametrized model to

'mimic' RESP charges might be usefull for simple cases, but I do not

think it can be proposed as a general strategy. However, this is

clearly a convenient "black box" for new users.

In the Kollman group strategy, _the_ RESP charge model is the basis of

the strength of AMBER force fields. Rescent AMBER, GLYCAM, CHARMM

force fields use even more sophisticated/modified 'RESP' charge

derivation (high basis set, complex multi-conformation fitting

approach etc).

Once again, I do not understand how a parametrized model can reproduce

another complex model that is controlled with a lot of difficulties.

regards, Francois

F.-Y. Dupradeau

---

http://q4md-forcefieldtools.org/FyD/

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" (in the *body* of the email)

to majordomo.scripps.edu

Received on Sun Jun 29 2008 - 06:07:42 PDT

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