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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Received on Sun May 25 2008 - 06:07:18 PDT
