Rizzo Lab Information and Tutorials
From Rizzo_Lab
Contents
[hide]DOCK
- Online Users Manual
- Tutorials
- Benchmarking
- Developer's Info
- Testset Protocols
- Parameter List/Explanations
- Scoring Functions
- Example Input Files
- DOCK Abbreviations Guide
- Advanced Dock Utilities/Information
- DOCK6 POSE Reproduction
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
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)
- ZINC12 Database
- ZINC15 Database
- Families in the Protein Databank
- Automated Family generation from PDB
- Drug-like organic molecules
Conversion between file types
Setting up accounts
AutoDock4
AutoDock Vina
Miscellaneous
- How to write Makefiles
- X-Win32
- CVS Commands
- Ethernet Cables
- Sequence alignment
- Making images for publication
- Lab-designed code and programs
- Server Administration
- Amber on Seawulf (compilation)
- Cluster compilations
- NAMD on Seawulf
- Semester Checklist
- Wiki Editing
- Other Meetings
- Seawulf Cluster Assessment
- Formatting your Thesis
- Setting up insurance through Research Foundation
