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
--
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Dr. Vlad Cojocaru
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e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Sun May 25 2008 - 06:07:47 PDT
