RE: AMBER: Dihedral Energy calculation

From: Junmei Wang <>
Date: Tue, 1 Mar 2005 12:57:49 -0600

The torsional angle term takes a form of (0.5) * Vn * (1 + cos (n*phi -
gamma)). Here, n takes 1, 2, 3, 4 ...; Vn is the force constant for the
nth Fourier term (the 3rd Field); gamma is the phase angle (4th Field);
n is in the 5th Field of a torsional angle term. If n is a negative
number, the immediately followed term is also applied for the same
torsional angle (more than one Fourier terms for this torsional angle).
On the other hand, if n is a positive number, the followed term is for
another torsional angle. I hope I made it clear.

Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649

        Dear Amber Users,
        I am calculating the diheral energy of a small molecule for
which I am using gaff.dat of Amber 8. I have noticed that some of the
dihedral are repeated with different values. for example
        c3-c2-c2-c3 1 6.65 180.0 -2.
Junmei et al, 1999
        c3-c2-c2-c3 1 1.90 180.0 1.
Junmei et al, 1999
        c3-c3-c3-c3 1 0.18 0.0 -3.
Junmei et al, 1999
        What basis is used for the calculation of such dihedral (whether
all or some are used) and how it is done in Amber.


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Received on Tue Mar 01 2005 - 19:53:01 PST
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