Merge pull request #594 from RosettaCommons/rhiju/fa_stack_ext
Rhiju/fa stack ext
Introducing potential energy function fixes for 'over-stacked' RNA conformations:
• fa_stack_sol: penalty for desolvating water stacked on nucleobases
• fa_stack_LR: an even more long-ranged bonus for water-mediated stacking of atoms on nucleobases.
• Shape and depth of these potentials partially calibrated based on PMF of water around adenosine, computed through Amber MD calcs by @fcchou, @sripakpa, and K. Beauchamp in my lab.
• Not yet checked on benchmark cases.May help 'solve' at high resolution:
UUCG loop (which always overstacks the G, leaving an internal void)
1CSL rev RRE element (whose lowest energy solution brings a bulged nucleobased into the helix, leaving a weird void)
T-loops, which always collapse a pocket that should accept a separate intercalating base. • Have not put in derivatives of new terms.
Tests on motifs above & putting in derivs might be of interest to @calebgeniesse or @kkappel1 later in the summer.