Difference between revisions of "Rizzo Lab Information and Tutorials"

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== DOCK ==
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{| cellpadding=0 width=90%
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*[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm Online Users Manual]
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*[[Tutorials]]
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*[[Benchmarking]]
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*[[Developer's Info]]
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*[[Testset Protocols]]
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*[[Parameter List/Explanations]]
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*[[Scoring Functions]]
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*[[Example Input Files]]
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*[[DOCK Abbreviations Guide]]
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*[[Advanced Dock Utilities/Information]]
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*[[DOCK6 POSE Reproduction]]
 +
|}
 +
 
== Visualization Software ==
 
== Visualization Software ==
 
*[[Chimera]]
 
*[[Chimera]]
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== Basic Linux Tools==
 
== Basic Linux Tools==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
|[[Unix]]
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*[[Unix]]
|[[vi ]]
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*[[vi ]]
|[[sed - Stream Editor in Unix]]
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*[[sed - Stream Editor in Unix]]
|-
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*[[Slick awk tricks]]
|[[Stupid awk tricks]]
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*[[Ways to remove the first line]]
|[[Ways to remove the first line]]
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*[[PBS Queue]]
|[[PBS Queue]]
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*[[gdb (GNU Debugger)]]
|-
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*[[Common Errors - ctrl M]]
|[[gdb (GNU Debugger)]]
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*[[C Shell Scripting]]
|[[Common Errors - ctrl M]]
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*[[Unix find]]
|[[C Shell Scripting]]
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*[[Which Unix Distribution?]]
|-
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*[[rsync]]
|[[Unix find]]
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*[[MPICH]]
|[[Which Unix Distribution?]]
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*[[Secure Shell (ssh)]]
|[[rsync]]
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*[[Archiving old data]]
|-
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*[[valgrind]]
|[[MPICH]]
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*[[Ghostscript]]
 
|}
 
|}
  
== DOCKing ==
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== Molecular Dynamics ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
|[[DOCK Tutorials]]
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*[[AMBER Tutorials]]
|[[Testset Protocols]]
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*[[AMBER TI Tutorials]]
|[[Scoring Functions]]
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*[[AMBER Lipid Tutorials]]
|[[Sampling Methods]]
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*[[AMBER tricks]]
|-
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*[[NAMD tutorial]]
|[[ZINC Database]]
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*[[NAMD Amber inputs]]
|[[Installing DOCK]]
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*[[per-residue energy decompositions]]
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*[[nonstandard residues prep]]
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*[[ptraj]]
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*[[Blocked Standard Error of the Mean]]
 
|}
 
|}
  
== Molecular Dynamics ==
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== GROMACS ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
|[[AMBER Tutorials]]
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* [[Compiling GROMACS on Cluster]]
|[[AMBER tricks]]
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* [[MD Simulation: Protein in Water]]
|-
 
|[[NAMD tutorial]]
 
|[[NAMD Amber inputs]]
 
|-
 
|[[ptraj]]
 
 
|}
 
|}
[http://www.ams.sunysb.edu/~tbalius/NamdandDockonNYBlue.pdf NAMD and DOCK on BlueGene ]
 
  
 
== Monte Carlo ==
 
== Monte Carlo ==
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== Analysis Tools ==
 
== Analysis Tools ==
 +
* [[Analysis Tools Repository]]
 
* [[MATLAB]]
 
* [[MATLAB]]
 
* [[Octave]]
 
* [[Octave]]
 
* [[R - Statistical Computing]]
 
* [[R - Statistical Computing]]
* [[Xmgrace]]
 
 
* [[gnuplot]]
 
* [[gnuplot]]
 
* [[pylab]]
 
* [[pylab]]
  
 
== Databases ==
 
== Databases ==
*[http://129.43.27.140/ncidb2/ NCI (ligand database)]
+
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem (ligand database)]
 
*[http://webbook.nist.gov/chemistry/ NIST (small molecule database)]
 
*[http://webbook.nist.gov/chemistry/ NIST (small molecule database)]
*[http://blaster.docking.org/zinc/ ZINC (ligand database)]
+
*[[ZINC12 Database]]
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*[[ZINC15 Database]]
 
*[[Families in the Protein Databank]]
 
*[[Families in the Protein Databank]]
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*[[Automated Family generation from PDB]]
 
*[[Drug-like organic molecules]]
 
*[[Drug-like organic molecules]]
 
== BlueGene ==
 
{| cellpadding=0 width=90%
 
| [[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]]
 
| [[BlueGene LoadLeveler Jobs with Multiple Steps (Chain Jobs)]]
 
|-
 
| [[scp files from cluster to NYBlue]]
 
| [[Get time for job completion]]
 
|}
 
  
 
== Conversion between file types ==
 
== Conversion between file types ==
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* [[NAMD to mol2 ]]
 
* [[NAMD to mol2 ]]
 
* [[pdb to mol2]]
 
* [[pdb to mol2]]
 +
* [[SDF to mol2]]
  
 
== Setting up accounts ==
 
== Setting up accounts ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
| [[Getting a BNL Account]]  
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*[[Activating your Seawulf Account]]
| [[Activating your Seawulf Account]]
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*[[Rotation students Wiki]]
| [[Rotation students Wiki]]
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|}
 +
 
 +
== AutoDock4 ==
 +
{|
 +
*[[AutoDock4 Pose Reproduction Tutorial]]
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*[[AutoDock4 Crossdock]]
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*[[AutoDock4 Benchmark Results]]
 
|}
 
|}
 +
 +
== AutoDock Vina ==
 +
{|
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*[[AutoDock Vina Pose Reproduction Tutorial]]
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*[[AutoDock Vina Benchmark Results]]
 +
|}
  
 
== Miscellaneous ==
 
== Miscellaneous ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
| [[X-Win32]]  
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* [[How to write Makefiles]]
| [[CVS Commands]]
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* [[X-Win32]]  
| [[Ethernet Cables]]
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* [[CVS Commands]]
| [[Sequence alignment]]  
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* [[Ethernet Cables]]
|-
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* [[Sequence alignment]]  
| [[Visiting BNL]]
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* [[Making images for publication]]
| [[Making images for publication]]
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* [[Lab-designed code and programs]]
| [[Lab-designed code and programs]]
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* [[Server Administration]]
| [[Server Administration]]
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* [[Amber on Seawulf (compilation)]]
|-
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* [[Cluster compilations]]
| [[Amber on Seawulf (compilation)]]
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* [[NAMD on Seawulf]]
| [[NAMD on Seawulf]]
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* [[Semester Checklist]]
| [[Dell 5110cn Printer]]
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* [[Wiki Editing]]
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*[[Other Meetings]]
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*[[Seawulf Cluster Assessment]]
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*[[Formatting your Thesis]]
 +
*[[Setting up insurance through Research Foundation]]
 
|}
 
|}
  
== Insurance ==
+
==Archive==
[[Research Foundation]]
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*[[Legacy Info]]

Latest revision as of 10:27, 15 September 2020

DOCK

Visualization Software

Basic Linux Tools

Molecular Dynamics

GROMACS

Monte Carlo

Analysis Tools

Databases

Conversion between file types

Setting up accounts

AutoDock4

AutoDock Vina

Miscellaneous

Archive