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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*[[Example Input Files]]
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*[[Advanced Dock Utilities/Information]]
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|}
 +
 
== 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]]
|[[Secure Shell (ssh)]]
 
|[[Archiving old data]]
 
|-
 
|[[valgrind]]
 
|[[Ghostscript]]
 
|}
 
 
 
== Docking ==
 
{| cellpadding=0 width=90%
 
|[[DOCK Tutorials]]
 
|[[Testset Protocols]]
 
|[[Scoring Functions]]
 
|[[Sampling Methods]]
 
|-
 
|[[ZINC Database]]
 
|[[ZINC15 Database]]
 
|[[Installing DOCK]]
 
|[[Optimize Polar Hydrogens]]
 
|[[Virtual Screening Protocol]]
 
|-
 
|[[Sphere Generation]]
 
|[[DOCK Compilation]]
 
|[[Virtual Screening Protocol on BlueGene (IGF-IR system)]]
 
|[[DOCK Benchmarking]]
 
|[[Release]]
 
 
|}
 
|}
  
 
== Molecular Dynamics ==
 
== Molecular Dynamics ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
|[[AMBER Tutorials]]
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*[[AMBER Tutorials]]
|[[AMBER TI Tutorials]]
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*[[AMBER TI Tutorials]]
|[[AMBER Lipid Tutorials]]
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*[[AMBER Lipid Tutorials]]
|[[AMBER tricks]]
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*[[AMBER tricks]]
|-
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*[[NAMD tutorial]]
|[[NAMD tutorial]]
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*[[NAMD Amber inputs]]
|[[NAMD Amber inputs]]
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*[[per-residue energy decompositions]]
|-
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*[[nonstandard residues prep]]
|[[per-residue energy decompositions]]
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*[[ptraj]]
|[[nonstandard residues prep]]
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*[[Blocked Standard Error of the Mean]]
|-
 
|[[ptraj]]
 
|-
 
|[[Blocked Standard Error of the Mean]]
 
 
|}
 
|}
  
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* [[Octave]]
 
* [[Octave]]
 
* [[R - Statistical Computing]]
 
* [[R - Statistical Computing]]
* [[Xmgrace]]
 
 
* [[gnuplot]]
 
* [[gnuplot]]
 
* [[pylab]]
 
* [[pylab]]
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*[http://pubchem.ncbi.nlm.nih.gov/ PubChem (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)]
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*[[ZINC12 Database]]
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*[[ZINC15 Database]]
 
*[[Families in the Protein Databank]]
 
*[[Families in the Protein Databank]]
*[[Automated Families generation from 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]]
 
| [[LoadLeveler 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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== 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]]
 
| [[Setting up RSA SecureID token]]
 
 
|}
 
|}
  
 
== Miscellaneous ==
 
== Miscellaneous ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
| [[X-Win32]]  
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*[[X-Win32]]  
| [[CVS Commands]]
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* [[CVS Commands]]
| [[Ethernet Cables]]
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* [[Ethernet Cables]]
| [[Sequence alignment]]  
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* [[Sequence alignment]]  
|-
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* [[Making images for publication]]
| [[Visiting BNL]]
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* [[Lab-designed code and programs]]
| [[Making images for publication]]
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* [[Server Administration]]
| [[Lab-designed code and programs]]
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* [[Amber on Seawulf (compilation)]]
| [[Server Administration]]
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* [[Cluster compilations]]
|-
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* [[NAMD on Seawulf]]
| [[Amber on Seawulf (compilation)]]
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* [[Semester Checklist]]
| [[Cluster compilations]]
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* [[Wiki Editing]]
| [[NAMD on Seawulf]]
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*[[Other Meetings]]
| [[Dell 5110cn Printer]]
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*[[Seawulf Cluster Assessment]]
|-
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*[[Formatting your Thesis]]
| [[Semester Checklist]]
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*[[Setting up insurance through Research Foundation]]
| [[Wiki Editing]]
 
|-
 
|[[Stony Brook Joint Group Meetings in Computational Structural Biology]]
 
|[[Other Meetings]]
 
|[[Seawulf Cluster Assessment ]]
 
 
|}
 
|}
  
== Formating Word Documents ==
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==Archive==
 
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*[[Legacy Info]]
[[Formating your Thesis]]
 
 
 
== Insurance ==
 
[[Research Foundation]]
 

Latest revision as of 11:59, 5 February 2019

DOCK

Visualization Software

Basic Linux Tools

Molecular Dynamics

GROMACS

Monte Carlo

Analysis Tools

Databases

Conversion between file types

Setting up accounts

Miscellaneous

Archive