Rizzo Lab Information and Tutorials
From Rizzo_Lab
Contents
Visualization Software
Basic Linux Tools
Docking
Molecular Dynamics
AMBER Tutorials | AMBER TI Tutorials | AMBER tricks |
NAMD tutorial | NAMD Amber inputs | |
per-residue energy decompositions | nonstandard residues prep | |
ptraj |
error analysis
Blocked Standard Error of the Mean
GROMACS
Compiling GROMACS on Cluster |
MD Simulation: Protein in Water |
Monte Carlo
Analysis Tools
Databases
- PubChem (ligand database)
- NIST (small molecule database)
- ZINC (ligand database)
- Families in the Protein Databank
- Automated Families generation from the Protein Databank
- Drug-like organic molecules
BlueGene
Conversion between file types
Setting up accounts
Getting a BNL Account | Activating your Seawulf Account | Rotation students Wiki | Setting up RSA SecureID token |