Difference between revisions of "Rizzo Lab Information and Tutorials"

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[[Outdated Info]]
[[Legacy Info]]

Revision as of 11:58, 4 February 2019

Visualization Software

Basic Linux Tools

Unix vi sed - Stream Editor in Unix
Stupid 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


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

De Novo Design (DOCK_DN) Small Molecule Evolution (DOCK_GA)

Molecular Dynamics

AMBER Tutorials AMBER TI Tutorials AMBER Lipid Tutorials AMBER tricks
NAMD tutorial NAMD Amber inputs
per-residue energy decompositions nonstandard residues prep
Blocked Standard Error of the Mean


Monte Carlo

Analysis Tools



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


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

Formating Word Documents

Formating your Thesis


Research Foundation


Legacy Info