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)
  where phase = 1.0 or -1.0, and pn = 1,2,3,4, or 6
2>. e = pk*( 1.0+cos(pn*phi-phase) ----- the old energy form,
if phase angle is other than 0 or pi then assume this angle.

Taking CT-CT-CT-CT in parm99.dat as an example,
CT-CT-CT-CT 1 0.18 0.0 -3. Junmei et al, 1999
CT-CT-CT-CT 1 0.25 180.0 -2. Junmei et al, 1999
CT-CT-CT-CT 1 0.20 180.0 1. Junmei et al, 1999

should the total torsional energy for this dihedral be one of the two forms:
a. (pk1*(1 + phase*Cos[pn1*phi ]) + pk2*(1 + phase*Cos[pn2*phi ]) + pk3*(1 + phase*Cos[pn3*phi]))
b. (pk1*(1 + Cos[pn1*phi - phase1]) + pk2*(1 + Cos[pn2*phi - phase2]) + pk3*(1 + Cos[pn3*phi - phase3]))

where pk1 = 0.18; pk2 = 0.25; pk3 = 0.20; phase1 = 0; phase2 = Pi; phase3 = Pi; pn1 = 1; pn2 = 2; pn3 = 3;
phase=1 or -1

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.
Thanks very much for your time.

-------
Jeffrey

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