AMBER Archive (2008)

Subject: Re: AMBER: ff99 and ff03 forcefield parameters

From: Peter Kiss (kisspeter1004_at_gmail.com)
Date: Fri May 23 2008 - 09:27:15 CDT

Dear Vlad,
Thank you for your response, I'm really very grateful for it.
A know that the ff99SB force field is a reparametrization of the original
ff99, and a read the paper. In this forcefield the babckbone dihedrals were
refitted again at LMP2/cc-pVTZ(-f)//HF/6-31G* theory of level. And the
charges were the same as in ff94 (HF/6-31g*//HF/6-31G*).And the side chain
torsional parameters came from the previous ff94 forcefield (where the enrgy
profiles cam from MP2/6-31G* level)?.
As far as i know, in ff03 the backbone parameters were derived at
MP2/cc-pVTZ//HF/6-31G**, and the charges at B3LYP/cc-pVTZ//HF/6-31G**.
These are clear for me.
In my case the missing torsional parameter are located in the side chain.
Therefore which level of theory should I use?
For a representative fragment I have to carry out HF/6-31G* optimization,
relax scan, and the energy from MP2/6-31G* calculation (as in ff94). After
that I have to calculate the resp charges for this small fragment at the
HF/6-31G*//HF/6-31G* theory (becuase the Etor=Eqm-Emm(non-bonded). And i
will obtain the appripriate parameters for the missing torsion. It is clear.
But after i obtained the parameters, should i calculate the
B3LYP/cc-pVTZ//HF/6-31G** charges for th whole molecule? But with other
charges the torsional parameters are also differnet. Or not?
Or I don't understand the parameter development?
Thank you for your response again, but your help will be very hepful.
Thanks,
Peter

2008/5/23 Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>:

> Maybe you want to take a look at the force field ff99SB instead of ff03 if
> you want to avoid any potential problems with compatibility between
> different charge sets and partially avoid the well known problems of ff99
> itself.
>
> vlad
>
>
>
> Vlad Cojocaru wrote:
>
> Dear Peter,
>
> Please take a look at the Duan et al. paper and see how exactly ff2003 was
> developed. You are right, only the main-chain parameters were refitted, the
> other torsions were kept from previous amber ff. The ff03 paper claims
> backward compatibility between ff03 charges and the Cornell et al charge
> set. If you look at previous mail threads on this list you'll find lots of
> discussion about using ff2003.
>
> The QM methods to derive amber ff parameters are described in the AMBER
> manual as well as in the references therein.
>
> GAFF is a generalized amber ff used for small molecules ..
>
> Testing of ff parameters is generally described in the papers that
> published those parameters. That is always a good starting point for ideas
> for further tests.
>
> Vlad
>
>
>
> Peter Kiss wrote:
>
> Dear Amber Developers and Users,
> Several days ago a posted a mail on the mailing list, but obtained no
> answers. Sorry for the new mail, but I'm still confused.
> If I have a modified amino acid with missing torsional parameter, and i
> would like to use it with ff03 forcefield, which QM calculations should is
> use?
> As far as I know, in the ff03 forcefield only the backbone dihedral were
> refitted, but the charge scheme is b3lyp/cc-pvtz//hf-631g**. Am I correct?
> But the dihedral parameters of the sidechains are the same as in the ff99
> forcefield., where HF/6-31G*//HF/6-31G* charges were applied.
> My questions are s follows:
> Why were the side chain torsional parameters not refitted in the ff03
> forcefield, with another charge model?
> Which ab initio calculations should I use for torsional paremeter
> development, and for the charges calculations?
> Or, alternatively, may I use the parameters from the GAFF forcefield? If
> yes, minimization, small molecular dynamics calculations, dipole
> moment/vibrational frequency comparison are enough parameters in order to
> confirm the goodness of parameters?
> Thank you for your help in advance!!!!
> Peter
>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuterhttp://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuterhttp://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
>

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