Dear Amber Friends,
I have a question about the general procedure of
generating the charges for non-standard
amino acids. The all_amino94.in file of the Amber
distribution contains for each AA the backbone atoms
NH-Calpha-CO plus the corresponding side chain atoms.
For non-charged AAs the given charges add up to zero
and they, somehow, also describe the bonding between
the AAs.
To account for these bonds, the esp is generated from the HF
wave function of a system containing additional atoms.
An easy case would be NH2-Calpha-COOH. These
additional atoms are then removed and the point
charges for the smaller systems are fitted to
the esp of the larger one, thereby the total charge
is kept zero (in the resp procedure).
Now the question:
What's the best (or standard) system for the generation
of the esp? (How many additional atoms/groups at each end)
What's the best way to do the cutoffs? Apparently the
charges of the backbone atoms are set to some default
values. That means that the sidechain charges must
compensate for the esp of the extra atoms of the
HF calculation.
Any explanations or pointers to literature are very much
appreciated.
Uwe
Received on Wed Oct 31 2001 - 05:46:15 PST
