Introduction
|
|
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
|
|
QSM: The Quantum String Method
|
|