On Aug 9, 2013, at 2:54 PM, "egeh00" <egeh00.aol.com> wrote:
> Dear all,
>
> I am puzzled about the two items, SCEE and SCNB. I know that SCEE is 1.2 and SCNB is 2.0 in GAFF as default values. And I also know LJ potential should be divided by SCNB and Coulomb should be divided by SCEE to get the final potential energy. Additionally, I know the SCEE and SCNB of many dihedrals in Glycam are both are 1.0. But I do not understand the meaning of the two items. People and modify the Vn in the dihedral equations to get a proper result, why do they add the two additional calculations? And if I parameterize certain dihedral, how can I get a proper Vn for the dihedral? should I consider the effect of SCEE and SCNB?
There are three bonded potentials in the Amber force field. You have bonds that account for the 1-2 interactions, angles that account for the 1-3 interactions, and torsions or dihedrals that account for the 1-4 interactions. The bond and angle terms are assumed to account for the full interactions between the involved atoms, so the non-bonded terms are not calculated between those atoms.
The torsion terms are not expected to account for the full interactions between the 1-4 pairs, so the electrostatic and van der waals interactions are still included (but scaled by some factor). Therefore the full torsion potential is a sum of all the terms in the Fourier series that makes up the torsion term plus the effects of the 1-4 nonbonded terms and the 1-4 van der waals and 1-4 electrostatic terms.
Therefore, you need to take the 1-4 nonbonded terms into account when you are parametrizing torsion terms yourself.
HTH,
Jason
P.S. the scaling factors scee and scnb have nothing to do with scaling the Vn terms.
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Received on Fri Aug 09 2013 - 16:00:03 PDT
