

AMBER Archive (2008)Subject: AMBER: from dihe parameters to torsional energy From: Jeffrey (jeffry20072008_at_yahoo.cn)Date: Wed Dec 17 2008  03:15:17 CST
Dear all,
I would like to figure out how dihedral parameters are used to calculate the torsional energy. After checking the subroutine subroutine ephi (src/nmode/ephi.f), I found two expressions were adopted for the dihedral energy:
1>. e = pk(ic) * (1.0+phase*cos(pn(ic)*phi)
Taking CTCTCTCT in parm99.dat as an example,
should the total torsional energy for this dihedral be one of the two forms:
where pk1 = 0.18; pk2 = 0.25; pk3 = 0.20; phase1 = 0; phase2 = Pi; phase3 = Pi; pn1 = 1; pn2 = 2; pn3 = 3;
Another question is how to output each energy term in AMBER to check if I have assigned a correct form of the expression?
Any suggestion is greatly appreciated.

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