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Revisions №57948

branch: master 「№57948」
Commited by: Rhiju Das
GitHub commit link: 「be58b21826f99acf」 「№594」
Difference from previous tested commit:  code diff
Commit date: 2015-06-30 01:03:05

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.

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