Hi, can you tell me how the energy value olde in the example script http://salilab.org/modeller/manual/node264.html (olde, dstate) = self.energy(state) is calculated? For an restraints file with N (physical.bond, physical.ca_distance, ...) entries in it, how does the formula look like: sum_i^N log(rsr_i), where rsr_i is defined as in http://salilab.org/modeller/manual/node469.html? Are there any scaling factors?
Best regards Armin
On 06/12/2012 08:58 AM, Armin Meier wrote: > can you tell me how the energy value olde in the example script > http://salilab.org/modeller/manual/node264.html > (olde, dstate) = self.energy(state) > is calculated?
This is described in a fair amount of detail in the appendix to the manual starting at http://salilab.org/modeller/9.10/manual/node465.html
If you need more detail, check out the 1993 JMB paper (also linked from the manual).
Any scaling factors used are shown in the log file.
Ben Webb, Modeller Caretaker