Can someone provide an explanation about converting Modeller's dihedral
restraints into plain psi/phi/omega angles? I have read through the
manual and have an intuitive feel for the way Modeller calculates these
values, but there are so many columns in the output file that I still am
not able to decipher it. So my question is is what columns in the
restraint file correspond to dihedral angles and their deviations, and
how do I convert them back to numbers in the -180 to 180 range.
The angles are in radians, so the conversion should be straightforward.
The deviations are calculated when the energy is calculated, so you
can't read them out of the restraints file.
This creates a restraint with (in order) form 7 (cosine potential),
periodicity 1, feature 3 (dihedral angle), group 3 (cosine dihedral
potential), acting on 4 atoms, with 2 parameters. The indices of the 4
atoms are 5, 4, 2 and 3, and the parameters (as in CHARMM, the phase and
force constant) are 3.1416 (i.e. pi) and 1.4000.