On Wed, Feb 17, 2016 at 10:56 PM, Jose luis Borioni <joseborioni.gmail.com>
wrote:
> Dear users,
> In my MD simulation I can see cation-pi interactions between a protonated
> tertiary amine of the ligand and a tryptophane of the receptor, and I have
> a doubt about how the MM force field represents these interactions.
> Anyone know this?
>
A combination of charge-charge and van der Waals interactions. Those are
the only non-bonded forces present in the Amber force field. The Amber
force field has a very simple functional form that you can look up just
about anywhere. Most of them omit common nonbonded exceptions (i.e.,
nonbonded interactions between pairs of atoms that form a bond or an angle
are omitted, and those between atoms forming a dihedral are scaled), but
other than that there is nothing "hidden" that goes into the simulation.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 19 2016 - 21:00:05 PST
