This lesson is still being designed and assembled (Pre-Alpha version)

LICHEM with Tinker and Gaussian: Glossary

Key Points

Introduction
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Structure Preparation
  • PROPKA is one way to calculate protonation states.

  • MolProbity can be used to check a structure for clashes, and make relevant ring flips.

  • Non-standard residues must have relevant hydrogens before parametrization.

  • For the final structure, LEAP will add hydrogens (and other missing sidechain atoms) based on residue definitions.

Molecular Dynamics and Clustering
  • An MD simulation can be broken down into 4 phases: minimization, heating, equilibration, and production.

  • DBscan can be very finicky, but it is a better approach to clustering.

  • Run k-means after DBscan. You can select the centroids from k-means as the random snapshots.

QM/MM Structure Preparation
  • Parameters are, and always be, the downfall of the computational chemist.

  • File numbering is a really common trouble spot, so pay close attention to what you’re working with and where.

DFP Optimizations and Strategies for Building a Suitable Product
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QSM: The Quantum String Method
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Glossary

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