A starting model for structure calculation is needed. For the following calculations an extended conformation is generated. This provides good local geometry but contains no information about the fold of the structure - this will be generated in the structure calculation stage. The extended conformation is calculated with the CNS task file generate_extended.inp.
cns_solve < generate_extended.inp > generate_extended.out [2 minutes]
The extended conformation is generated from the molecular topology information and initial random coordinates using an extensive series of minimization steps. The output coordinates form an extended conformation:
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| Extended conformation (two separate chains in red and green) |