AMBER Archive (2008)

Subject: Re: AMBER: Antechamber/mopac am1-bcc charge

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jun 27 2008 - 04:07:45 CDT

Quoting Junmei Wang <junmwang_at_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_at_q4md-forcefieldtools.org> wrote:
>
>> Quoting Junmei Wang <junmwang_at_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_at_gmail.com
>>> >
>>> wrote:
>>>
>>> On Thu, Jun 26, 2008 at 4:33 PM, Junmei Wang <junmwang_at_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_at_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_at_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_at_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
>>>>
>>>
>>
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>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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