AMBER Archive (2009)

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

From: Marek Maly (
Date: Wed Jul 01 2009 - 10:47:04 CDT

Dear Francois,

thank you very much for the additional info !



Dne Tue, 30 Jun 2009 09:31:53 +0200 FyD <>

> Dear Marek,
>> 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.
> Yes
>> 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.
> 200 % agree with you ;-)
>> 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) ?
> I do not know.
>> 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.
> Yes, do your own study.
>> 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) ?"
> Here the Antechamber developers should answer.
> My understanding is that the number of force field (FF) atom types in
> GAFF is superior than these in parm99. Consequently, this might generate
> problems when you want to generate FF atom type automatically; I mean
> for parm99, you will get "blanks"...
>> 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 ?
> This is the reason why the FF libraries in R.E.DD.B. are FF atom types
> independent; i.e. FF atom types are always added using a LEaP script.
> See for instance:
> Personnally, I always use parm99 FF atom types for organic
> molecules/protein/nucleic acid and add FF atom types manually; pick up
> only _classical_ force field parameters from GAFF (bond & angle force
> constants, aromatic dihedrals) and adapt them to parm99 way. Get
> equilibrium values from high ab initio geometry optimization or X-ray
> structures (not from GAFF). Key dihedrals are always refitted (not
> obtained from GAFF).
> What you said above summarize exactly the problem "so some inacuracy
> regarding to specific molecules is "penalty" for it's
> transferability/universality". When you use GAFF automatically all is
> fine if your molecule has been well parametrized but you do not know if
> it was indeed well parametrized...
> Just my personal opinion: Others might have other experiences.
> regards, Francois
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