AMBER Archive (2008)

Subject: Re: AMBER: ff99 and ff03 forcefield parameters

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri May 23 2008 - 04:43:38 CDT

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 Reuter
> http://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 Reuter
http://www.eml-r.org
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