AMBER Archive (2006)

Subject: AMBER: Curve fitting during dihedral parameter calculation

From: Prashanth Athri (
Date: Thu Oct 19 2006 - 14:15:21 CDT

Dear Users: I wanted to know if there is a 'recomended procedure', and a reference for the same, to fit a Quantum derived energies to the fourier cosine that Amber uses to model torsion potentials. As in once we have a list of energies for the torsion 'theta' about the dihedral ZZ-ZA-ZS-ZD, for 0 to 360 in, say, 10 degree intervals-- to get the V1, V2, etc we fit this curve to Ptot: Ptot(theta)= P2(theta) + P6(theta) where, P2(theta) = V2/2 (1+ cos(2*theta-phase)) P6(theta) = V6/2(1+ cos(6*theta-phase)) and more terms, if needed. [P1,P3,P4] So, my question is whats the best curve fitting protocol to do this. Is there an algorithm? Does someone have a pseudocode for the same? Thanks in advance. Regards, Prashanth
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