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With the latest version of YANK, running the p-xylene-implicit example, via:
yank prepare binding amber --setupdir=setup --ligand="resname BEN" --store=output --iterations=1000 --restraints=harmon…
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This is actually pretty complicated, so won't finish tonight. Will review my progress with you tomorrow.
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In the original version with integrate also doing a minimization/annealing, this process was called equilibration.
Question: Should there be an annealing option, as well as an equilibration option?
T…
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When searching for a compound, for example in this case Erythrose, using the SMILES formula obtained from OpenPHACTS (http://ops.rsc.org/OPS1782071), it brings up the error message "Internal server er…