On Thu, Jan 10, 2013, Dr. Vitaly Chaban wrote:
>
> Can anyone give me a reference, where the derivation of AMBER FF
> *bonded parameters* in described in most details?
The description of bonds and angles is in the original Cornell et al paper,
JACS 117:5179, 1995. Since then torsion parameters (which reflect both bonded
and non-bonded interactions) have been modified a number of times, as outlined
in the AmberTools Reference manual.
Above is for standard proteins and nucleic acids. There is a lot of info
about bonded parameters for other molecules in the GAFF papers, e.g. J.
Comput. Chem. 25:1157,2004.
...dac
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Received on Fri Jan 11 2013 - 07:00:02 PST
