AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jun 27 2008 - 17:02:21 CDT

OK, simplicity might br illusory in this area, as I also said. One is
not prevented by current theories to try to be rigorous, however. You
know the work by your co-nationals on tetracycline (JACS 2008, 130,
114). How many others are willing (or allowed) to invest so much time
for every new family of "unusual" compounds they want to investigate?

Personally, I see the danger to be simplistic, but I am tankful for
GAFF. More than that, what I would like to see is a comparison of the
said work on tetracycline carried out with GAFF. What about if that
turns out in a substantial agreement of the results (and, of course,
agreement with experiments, if they exist or can be done)?

If not, unless it is an oddness for such a class of compounds. we
should be suspicious about any simulation carried out for "unusual"
compounds with simplified FF. Not a good perspective, also because
packages for electronic calculation are not well devised to help
setting up a fitting FF. They can do that, but along tricky work.

Well, I feel that existing literature comparing in a clear,
unequivocal, practical way "rigorous" with "simplified" approaches
should be put at the forefront. This is a wish by the common user, as
I am. If that level of transparency was not reached, it should be
attempted. Unattractive work, I agree.

francesco

On Thu, Jun 26, 2008 at 10:53 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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-- 
Dr Francesco Pietra
Professor of Chemistry
Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
Palazzo Ducale
55100 Lucca (Italy)
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