[gmx-users] dihedral angle barrier height

atanu das samrucu at yahoo.co.in
Wed Oct 11 09:03:20 CEST 2017

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)? 
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.

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