After a conformational search is complete, the coordinates are left in the same state as they were before the search began. The COOR SAVE END option is ignored.
The DEBUG option controls the setting of the
debug variable. The default value of 0 prints no debugging information.
Larger values print more information. A debug value of 2 is good for
getting an idea of why a search failed without generating too much
output. The maximum value of 5 will fill a disk as fast as the computer
can write to it. See Debug Command, for more details.
The NOSOPT option will turn off an optimization in the sidechain FIRST placement method. See Sidechain Degree of Freedom, for more details. This option is used only for debugging.
The SEED option sets the seed for the random number generator used by RANDOM evaluation option, see Search Method Options. When CONGEN runs in parallel, each process gets a copy of this seed. The seeds are not saved in the restart file, so a run interrupted and restarted will not generate the same random structures.
The options, EPCONS and EJCONS, are used to apply dihedral angle constraints, see Harmonic Dihedrals, or NMR J coupling constraints, see NMR Constraints, in the generation of atomic positions. This functionality is experimental, and requires some care in its application. Both options specify the maximum allowed energy for constructing an atom which is either the first or last atom in the specification of a dihedral angle or J coupling constraint, and whose antecedent atoms are also in the specification of the constraint. No dihedral angle constraints are applied if the J coupling constraint derives from an average over multiple conformations or if the J's are joined. For example, if you have a J coupling constraint for a backbone phi torsion angle, then the construction of the backbone carbonyl carbon at the end of that constraint may be affected. The option, EPCONS, is used to select the dihedral angle constraints. The option, EJCONS, is used for the J coupling constraints. Both of these options specify energies in kcal/mole. If these values are very large, then they will not have any affect on the conformational search. At the present time, these constraints are not coupled with van der Waals avoidance when sidechains are constructed, see Sidechain Overview. If there is sufficient interest, they can be.