ChemServerComputational chemistry guides
Short, practical guides to the three workhorses of computer aided drug design. Each one explains the steps, the usual settings and the mistakes reviewers look for.
How to do molecular docking
Choose and prepare the protein, prepare ligands, set the grid box, run AutoDock Vina, validate by redocking and read the scores.
How to run an MD simulation
Force fields, solvation, minimization, NVT and NPT equilibration, production runs and analysis of RMSD, RMSF and MM/GBSA.
How to do a DFT calculation
Geometry, charge and multiplicity, functionals and basis sets, frequency checks, HOMO LUMO gaps, charges and spectra.