AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jun 28 2008 - 12:22:44 CDT

Yes, I know those papers, perhaps not so well mastered as they
deserve. What I am interested in is to clarify what you call a "black
box", that is comparing - in actual cases - the result of applying
RESP with respect to applying am1-bcc as provided by Antechamber. I
mean comparing for a demanding structure, like the tetracyclins, or
other ones, perhaps embedded in a lipidic membrane and even made as
ligands of proteins, just to make the system more complicate. How
would you react if the results turn out to lie in the statistics
expected for MD for both RESP and am1-bcc? The black box made
transparent. There are so many approximations and assumptions in
performing simulations that I would not be too surprised that there is
such an agreement. I am looking for such papers in the literature.
Curious if they do not exist. It would allow to take personal views
without any firm support. If the papers you mention were a clear cut
answer, why developing Antechamber with am1-bcc? It is becoming hot
here, worse quite humid.

Regards
francesco

On Sat, Jun 28, 2008 at 9:47 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
> Quoting Francesco Pietra <chiendarret_at_gmail.com>:
>
>> OK, simplicity might br illusory in this area, as I also said.
>
> Yes.
>
> I think you could read some original papers from Kollman & coworkers.
> For instance, the paper corresponding to parm96.dat & parm98.dat. This is
> clearly explain that the strength of AMBER force fields is THE charge model,
> i.e. RESP and not Mulliken (at that time am1-bcc was not developped; I
> personally avoid am1-bcc because this is a black box).
>
> BEHIND the word "RESP" is not just picking a conformation and applying a 2
> stages fitting approach. On the contrary, a well defined strategy is
> defined:
> * rigorously define the conformation(s) used with well defined rules
> - small difference in energy between conformations, avoiding conformations
> with hydrogen bond(s), etc ... -
> * rigorously define the basis set used
> * rigorously define the 2 fitting approach
> This means a user has to pay the price (computer simulation time, time
> spent) to study the system (before MD simulation).
>
> This is the strength of the parm94, 96, 98 and 99 AMBER and GAFF force
> fields. Then, more complex strategies were applied such as in ff03 FF and
> Glycam FF, but still based on a RESP fitting approach.
>
>> 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?
>
> Well my personal opinion this is a normal work if one wishes to produce
> interesting papers.
>
>> Personally, I see the danger to be simplistic, but I am tankful for
>> GAFF.
>
> GAFF is based on the RESP charge model.
>
>> 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.
>
> Well, every user can learn, little by little. The AMBER mailing list helps a
> lot.
>
> More a user will spend time to prepare her/his FF (FF parameters; charge
> values - before MD simulation), more she/he will control/be able to
> understand her/his results after MD simulation.
>
> regards, Francois
>
>
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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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