Hi,
according to amber manual dihedral potential is calculated by following
formula: (Vbarrier/divider) ×[1+cos(periodicity×φ − phase)]
for example for this dihedral :
hn-n -c -o 1 2.50 180.0 -2.
hn-n -c -o 1 2.00 0.0 1.
total potential is that:
Etorsion = 2.00×[1+cos(1×φ −0.0)] +2.50×[1+cos(2×φ −180.0)]
my question is: in gaff, gaff2, ff9SB some dihedrals has 0 Kb. For example
for this dihedral:
First term : C -N -CT-C 1 0.00 0.0 -4. (Kb=0)
Second term: C -N -CT-C 1 0.42 0.0 -3. (Kb=0.42)
=> Etorsion = 0.00×[1+cos(1×φ −0.0)] +0.42×[1+cos(2×φ −00.0)]
It seems the first term which has Kb=0 value does not affect the result at
all Then why did they put this value there? What is the difference between
typing the first value which has 0 Kb and not typing ?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 05 2019 - 12:00:03 PST
