In the gaff.dat force field paramater,
there are different torsion values of n, gamma, vn_half for c3-c3-c3-c3
chains.
I consulted the Amber specification, and it says that if PN is negative, it
means that 'additional parameters have to be read'.
It was my understanding that the torsional energy of any given bond is
calculated in OpenBabel according to:
var tor = VectorTorsion(atom A, atom B, atom C, atom D);
cosine = Math.cos(DEG_TO_RAD*(n*tor-gamma));
phi1 = 1.0 + cosine;
energy = vn_half * phi1;
So I have
barrier # phase angle PN
c3-c3-c3-c3 1 0.18 0.0 -3. Junmei et al,
1999
c3-c3-c3-c3 1 0.25 180.0 -2. Junmei et al,
1999
c3-c3-c3-c3 1 0.20 180.0 1. Junmei et al,
1999
so if I have four c3 atoms joined together, how do I determine which one to
use? I created a c3-c3-c3-c3 chain and verified in OpenBabel that the
torsion uses parameters from the line:
c3-c3-c3-c3 1 0.18 0.0 -3. Junmei et al,
1999
and my debugger tells me that n = 3. However I am not sure how this value
of n is calculated in the first place, and why it looks up the value for PN
= n = -3 when n is supposed to be 3.
So to sum up:
- how to find n?
- how to determine which vn_half, n, gamma values to use?
Thanks,
Eric
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