Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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== Molecular Dynamics == | == Molecular Dynamics == | ||
{| cellpadding=0 width=90% | {| cellpadding=0 width=90% | ||
| − | + | *[[AMBER Tutorials]] | |
| − | + | *[[AMBER TI Tutorials]] | |
| − | + | *[[AMBER Lipid Tutorials]] | |
| − | + | *[[AMBER tricks]] | |
| − | + | *[[NAMD tutorial]] | |
| − | + | *[[NAMD Amber inputs]] | |
| − | + | *[[per-residue energy decompositions]] | |
| − | + | *[[nonstandard residues prep]] | |
| − | + | *[[ptraj]] | |
| − | + | *[[Blocked Standard Error of the Mean]] | |
| − | |||
| − | |||
| − | |||
| − | |||
|} | |} | ||
Revision as of 11:05, 4 February 2019
Contents
Visualization Software
Basic Linux Tools
Docking
De novo Design using DOCK
Molecular Dynamics
GROMACS
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 |
