Difference between revisions of "Rizzo Lab Information and Tutorials"
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Revision as of 15:14, 26 June 2014
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 |
