

AMBER Archive (2008)Subject: RE: AMBER: from dihe parameters to torsional energy From: Ross Walker (ross_at_rosswalker.co.uk)Date: Wed Dec 17 2008  10:36:14 CST
Dear Jeffrey,
My understanding of this is that the two equations are the same thing given
The 'real' equation as written in terms of the AMBER force field is:
e = pk(1.0+cos(pn*phiphase))
If my trigonometry is correct (it is early in the morning so buyer beware),
e = pk(1.0+cos(pn*phi)*cos(phase))
You would not want to do this computationally since cos functions are
Hence the above equation becomes:
e = pk(1.0(+/)cos(pn*phi))
The net result though is that it is the same function as the original
Hence the short answer is that it shouldn't matter which route through the
If you want a list of dihedrals from the prmtop then you can run:
$AMBERHOME/exe/rdparm prmtop
and type 'dihedrals'
This will list everything from which given a set of coordinates and the
I hope that helps,
All the best
Ross
From: owneramber_at_scripps.edu [mailto:owneramber_at_scripps.edu] On Behalf Of
Dear all,
I would like to figure out how dihedral parameters are used to
1>. e = pk(ic) * (1.0+phase*cos(pn(ic)*phi)
Taking CTCTCTCT in parm99.dat as an example,
CTCTCTCT 1 0.18 0.0 3. Junmei et al,
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
b. (pk1*(1 + Cos[pn1*phi  phase1]) + pk2*(1 + Cos[pn2*phi  phase2]) +
where pk1 = 0.18; pk2 = 0.25; pk3 = 0.20; phase1 = 0; phase2 = Pi; phase3 =
phase=1 or 1
Another question is how to output each energy term in AMBER to check if I
Any suggestion is greatly appreciated.
Thanks very much for your time.

Jeffrey

 
