AMBER Archive (2008)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jun 26 2008 - 15:53:20 CDT

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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