Ab Initio SA Starting from the Template

The example input file below shows how to produce a family of coordinates using ab initio simulated annealing starting from the template coordinate set (Nilges, Kuszewski, and Brünger, 1991). The example file is general and should work for all types of macromolcules, although it has been tested only for proteins up to 2400 atoms. Important parameters that the user might want to change are the simulated annealing starting temperature, the duration of the high-temperature stage, and the duration of the cooling stage. The protocol works well for proteins with up to about 1000 atoms. For 2000 atoms, the durations should be multiplied by a factor of about four. The filenames of the family of embedded coordinates are “sa 1.pdb" through “sa 10.pdb". The coordinate files contain useful information about the energies, restraint-satisfaction, and violations.

sa.inp