[gmx-users] dihedral angle barrier height
atanu das
samrucu at yahoo.co.in
Wed Oct 11 09:03:20 CEST 2017
Hi,
I am a bit confused about the value that I should take as the dihedral angle barrier height. I am using Amber03 forcefield. What I can understand so far from the ffbonded.itp file is that following are the parameters for psi and phi dihedral angles -----
N CT C N 9 180.0 2.86144 1 ; Amber03 N CT C N 9 180.0 6.08228 2 ; Amber03 N CT C N 9 180.0 1.93092 3 ; Amber03
C N CT C 9 0.0 4.25053 1 ; Amber03 C N CT C 9 180.0 1.44390 2 ; Amber03 C N CT C 9 0.0 0.94517 3 ; Amber03
Now, if I want to report the dihedral angle barrier height for a protein, what value should I choose? Can I use the value of kd as the barrier height? If so, should I choose the highest kd among the 6 kd values (i.e. 6.08 kj mol-1 rad-2)?
Or
Should I calculate using the equation ----
V_psi = 2.86(1+cos(1*180))+6.08(1+cos(2*180))+1.93(1+cos(3*180))V_phi = 4.25(1+cos(1*0))+1.44(1+cos(2*180))+0.94(1+cos(3*0))
V_total = V_psi + V_phi
Another point is that the angles are reported in degrees and the kds are reported in kj mol-1 rad-2.
ThanksAtanu
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