AMBER Archive (2009)

Subject: Re: [AMBER] Nonstandard molecules simulated with parm99EP ?

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Mon Jun 29 2009 - 15:48:52 CDT

Dear Francois,

thank you very much for your quick response !

I just took a look on the article which you suggested below. Unfortunately
the authors do not discuss much in detail why they prefared parm99 for
their experimental/computational "alcohol story"
. They just mention that GAFF provided unsatisfactory results in some
cases (MeOH, t-BuOH) which probably comes mainly from too low
value of the O-H force constant. On the other hand after choosing parm99,
this force constant was anyway subject of their reparametristion
(as well as in case of relevant charges) but probably already before this
reparametrisation parm99 behaves a little better than GAFF for
their molecular systems and relevant experiment data (FTIR spectra).
Intuitively this could be clear since GAFF parametrisation is based
on really wide set of suitable chosen molecules (200 if I am not wrong) to
cover wide variety of molecular structures,
so some inacuracy regarding to specific molecules is "penalty" for it's
transferability/universality.

So OK, this is one particular example, which describes that parm99 could
be for some class of non-nucl.acids/non-proteins molecules better
regarding to
specific experimental data than GAFF. Are there some another examples of
comparison of parm99/parm99EP versus GAFF in cases of
non-nuc.acids/non-proteins available
(especially some related to free energy of binding calculations) ?

Is there some general recommendation available to decide which forcefield
(ff99, ff99EP, GAFF) could be more suitable for the given "nonstandard"
molecule
regarding to given physical property ? Probably no and one should make
some short simulation tests.

But in this context there is still in the game my original question:

"How it is possible to force the antechamber to use some different
forcefield from GAFF ( like for example parm99EP
for parametrisation of the relevant residui (generating of PREPIN/FRCMOD
files) ?"

One possible way, although not much comfortable is of course to let the
antechamber generate PREPIN's/FRCMOD's with
GAFF forcefield atom types and then manually change this atomtypes to the
corresponding atomtypes from
desired forcefield (parm99/parm99EP) but as I mentioned before it is
really not the most comfortable way
which of course provide some chance to do mistakes on this level. So I
hope there is some easier (automatic) way how
to do this job or not ?

Thanks again to anyone for any additional comments.

Best,

   Marek

Dne Mon, 29 Jun 2009 20:28:19 +0200 FyD <fyd_at_q4md-forcefieldtools.org>
napsal/-a:

> Marek,
>
> If you read the paper describing parm99, it is explained that this FF
> was a first attempt in the direction of organic structures.
>
> If you look in R.E.DD.B. the project of C. Cezard
> Bulky Alcohols
> http://q4md-forcefieldtools.org/REDDB/projects/W-79/
> Author(s) Christine Cézard, Corey A. Rice and Martin A. Suhm
> Journal of Physical Chemistry A
> Year 2006 Volume 110 Page(s) 9839 - 9848
>
> The authors describe in their paper that parm99 was better than GAFF for
> what they wanted to study...
>
> regards, Francois
>
>
>> Dear Amber users,
>> recently I have read a very interesting article:
>>
>> http://pubs.acs.org/doi/abs/10.1021/ma062610a
>>
>> ( free download at http://www.mose.units.it (section PUBLICATIONS) )
>>
>> related to simulations of Naphthyridine-based dendrimers using Amber7
>> and parm99EP forcefield. The authors have obtained an excellent
>> agreement with
>> experimental binding energy results regarding to complexation with
>> small ligands
>> at dendrimer core in explicit solvent (10% CH3-CN and 90% CHCl3).
>> I was a little bit surprised since I thought that parm99EP forcefield
>> is devoted mainly to simulations of nucleid acids and proteins and for
>> simulations
>> of such "exotic" molecules like for example above mentioned class of
>> dendrimers, GAFF is more suitable.
>>
>> Unfortunately the authors didn't mention some important details - for
>> example how they
>> parametrised their dendrimers for Amber calculations in particular how
>> they succeeded
>> to create relevant PREPIN files using parm99EP forcefield.
>>
>> So I have just the simple technical question: How it is possible to
>> force the antechamber
>> to use some different forcefield from GAFF ( like for example parm99EP
>> ) for parametrisation of the
>> relevant residui (generating of PREPIN/FRCMOD files) ?
>>
>> Does anybody have positive experiences with usage of parm99/parm99EP
>> for simulations of some non-nucleic/non-protein
>> molecules or did someone even try to compare GAFF results with
>> parm99/parm99EP ones regarding to simulation of "nonstandard" molecules
>> ?
>> (By term "nonstandard" I mean here non-protein, non-nucleic acid)
>>
>> Thanks in advance for your feedback.
>>
>> Best,
>>
>> Marek
>
>
>
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