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Fixed script: was exiting after computing native energy!
New feature in TinkerRunner: now it can run "analyze" and "minimize" programs from the tinker package Fixed some bugs and improved TinkerRunner: - flushing instead of closing the log PrintWriter when throwing TinkerError exception. Before it would close and nothing more would get logged after the first error. - now writing command line to log - now flusing at the end of each runXXX() method New script computeEnergies for calculating energies of a set of decoys using tinker.
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