The construction of prolines is more involved than the other amino residues because of the ring. The approach used in CONGEN is to precompute a table of proline geometries based on the particular value of the phi torsion angle. When a ring with a particular phi angle is required, the table is linearly interpolated to find the geometry to use.
The geometries are determined using a model of just the ring
with two terminating methyl groups, specifically, 1,2-dimethyl
pyrrolidine. The geometry and energies for particular phi angles are
computed by constructing the ring with the given phi angle, setting a
torsion angle constraint (see Harmonic Dihedrals), with a high
force constant. Then, the ring is minimized, and the actual value of
phi, and the bond lengths, angles, and torsions needed to construct CB,
CG, and CD are used. In addition, the energy of system
e, the van
der Waals energy
evdw, and constraint energy
ec are stored
in the table.
This table is stored in the proline constructor file and has the following format:
title count (I5) phi,e,evdw,ec,(bond(i),theta(i),phi(i),i=1,3) (13F10.5)
count is the number of table entries.
phi is the phi
backbone torsion angle after minimization.
ec are given above. The triples of bonds, angles, and torsions
given the construction data needed to construct CB, CG, and CD, using
internal coordinates, C-N-CA-CB, N-CA-CB-CG, CA-CB-CG-CD,
A proline constructor file good for general use is stored in
CGDATA:PRO.CNS. See Emap, for a description of its
construction. The subroutine,
RDPROCONS, is used this