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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
