noe-way-jose
Probabilistic NOE module for PHAISTOS
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Options:
energy-noe = 1 # Activate energy-noe [number of occurrences] energy-noe-debug = 0 # Debug level energy-noe-weight = 1 # Weight used when summing energy terms energy-noe-weight-constant = 1 # Apply an extra weight factor (default is 1.0) energy-noe-active-restraints = 1 # Number of active restraints (default is 1) energy-noe-seamless = false # Seamless restraint switching -- experimental! (default is False) energy-noe-upl-filename = "/home/andersx/final.upl" # CYANA UPL formatted list of NOE contacts
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Input format is the CYANA UPL format, i.e.:
178 GLU H 179 GLU H 4.52 179 GLU H 180 LYS H 4.66 28 TYR H 28 TYR QD 3.613 28 TYR H 176 ILE QD1 5.532 27 VAL QG1 28 TYR H 4.128 27 VAL QG2 28 TYR H 4.12 28 TYR H 171 LEU H 3.829
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Only N out of all restraints are active at a time.
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The potential is the ROSETTA bounded potential explained here:
https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/de/d50/constraint_file.html http://www.pnas.org/content/suppl/2012/06/25/1203013109.DCSupplemental/Appendix.pdf
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Force constant simpy multiplies the potential by a scaling factor.
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Seamless restraint switching adds a bias, which connects potential surfaces when switching from one set of restraints to another. This effectively forces switching of restraints. Otherwise, they are sampled. This can be used to escape local minima in simulations.