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.
Best
Junmei
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
>>>
>>
>
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Received on Sun Jun 29 2008 - 06:07:34 PDT
