Difference between revisions of "Rizzo Lab Information and Tutorials"
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Revision as of 12:07, 4 February 2019
Contents
[hide]Visualization Software
Basic Linux Tools
- Unix
- vi
- sed - Stream Editor in Unix
- Slick awk tricks
- Ways to remove the first line
- PBS Queue
- gdb (GNU Debugger)
- Common Errors - ctrl M
- C Shell Scripting
- Unix find
- Which Unix Distribution?
- rsync
- MPICH
- Secure Shell (ssh)
- Archiving old data
- valgrind
- Ghostscript
Docking
- DOCK Tutorials
- Covalent DOCK
- Testset Protocols
- Scoring Functions
- Sampling Methods
- 3D Analog Library Generation Using Pubchem and Zinc
- ZINC12 Database
- ZINC15 Database
- Installing DOCK
- Optimize Polar Hydrogens
- Virtual Screening Protocol
- Footprint Plot Visualization
- Sphere Generation
- DOCK Compilation
- Virtual Screening Protocol on BlueGene (IGF-IR system)
- DOCK Benchmarking
- Release
De novo Design using DOCK
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
- Blocked Standard Error of the Mean
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
- Setup ssh tunnel to NYBlue fen
- Get time estimate for free blocks
- Get Job ids to use for llcancel
- Submitting BlueGene Jobs
- Compiling Applications for BG/L
- LoadLeveler Chain Jobs
- scp files from cluster to NYBlue
- Get time for job completion
Conversion between file types
Setting up accounts
- Getting a BNL Account
- Activating your Seawulf Account
- Rotation students Wiki
- Setting up RSA SecureID token
Miscellaneous
- X-Win32
- CVS Commands
- Ethernet Cables
- Sequence alignment
- Visiting BNL
- Making images for publication
- Lab-designed code and programs
- Server Administration
- Amber on Seawulf (compilation)
- Cluster compilations
- NAMD on Seawulf
- Dell 5110cn Printer
- Semester Checklist
- Wiki Editing
- Stony Brook Joint Group Meetings in Computational Structural Biology
- Other Meetings
- Seawulf Cluster Assessment
