Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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|[[AMBER Tutorials]] | |[[AMBER Tutorials]] | ||
|[[AMBER TI Tutorials]] | |[[AMBER TI Tutorials]] | ||
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|[[AMBER tricks]] | |[[AMBER tricks]] | ||
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===error analysis=== | ===error analysis=== | ||
[[Blocked Standard Error of the Mean]] | [[Blocked Standard Error of the Mean]] | ||
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== GROMACS == | == GROMACS == | ||
Revision as of 12:26, 25 August 2014
Contents
Visualization Software
Basic Linux Tools
Docking
Molecular Dynamics
| AMBER Tutorials | AMBER TI Tutorials | AMBER Lipid 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 |
