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Hello Valerie--
> I tried using posDiffPot and simulationTools.minimizeRefine to
> regularize the atomic positions after adding CYSP-MTSL and protons to
> a crystal structure:
try changing your minimizeRefine call to
minimizeRefine([test],
refineSteps=50,
xplorPots=['BOND','ANGL','IMPR'])
best regards--
Charles
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