Dear list,
I've been attempting to simulate torsional energies as eloquently discussed
at the end of the Amber 8 manual using combined Fourier series terms.
For situations as simple as ethane, the situation only has explicit H-C-C-H
terms , nine paths, and "zero degrees" applies to any eclipsed situation.
So how does one handle a situation with two non-identical chiral carbons
that have nine different X1,2,3-C-C-X4,5,6 torsions?
x1-C-C-x4
x1-C-C-x5
x1-C-C-x6
x2-C-C-x4
x2-C-C-x5
x2-C-C-x5
x3-C-C-x4
x3-C-C-x5
x3-C-C-x6
I realize that one can arbitrarily assign a zero angle, and find the
difference between the QM energy profile and the MM profile(tortional terms
zeroed out), and parametrize the difference with a "single" Fourier series
expression. But I'm trying to calculate the torsional energy component for
such a torsion from the parameters that gaff provides for me, to determine
if the parameters provided by gaff are sufficient. (and to try to understand
more about what I am doing!). Basically, I want to know how to sum all the
nine torsional parameters that gaff provides for that torsion, given that
eclipsed and anti, etc. in this case depends which atoms you are talking
about.
Also, is there a simple way to do a dihedral coordinate energy scan in
amber??
Any help in this regard would be most welcome!!
Thanks so much.
Dean
Dr. Dean Cuebas dac012f.missouristate.edu,
Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 03 2010 - 17:30:02 PST
