On Thu, Sep 22, 2011 at 7:24 PM, Rajesh Raju <rajesh.raju.mail.chem.tamu.edu
> wrote:
> Dear AMBER users,
>
> I am just curios about to know how AMBER treats CH/pi, OH/pi NH/pi
> type of interactions and stacking interactions. Does the van der wall
> interatcion terms are sufficient enough to model stacking ch/pi and
> stacking interactions as the major compent of this interactions are
> dispersion forces..
>
There are no specific interaction types in the typical amber force field.
There are the bonded interactions (bond, angle, dihedral potential terms)
and nonbonded interactions (12-6 Lennard Jones VDW potential and standard
EEL potential, with the 1-2, and 1-3 nonbonded interactions not counted and
the 1-4 nonbonded interactions scaled). Any other empirically observed
interaction/force will have to be captured by one of those terms.
The formula written on Wikipedia (
http://en.wikipedia.org/wiki/AMBER) is
correct if the double-sum over the non-bonded pairs omits the terms I
mentioned above, and scales the 1-4 interactions.
Hope this helps,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 22 2011 - 17:00:02 PDT
