TACC+VINA+Work


 * Purpose**: this page is so that Dr. B, Christina and Alex can collaborate on getting VINA running on TACC (in serial or in parallel mode? - MPI or Serial using PyLauncher utility or just Launcher utility)

SAVE RELEVANT FILES TO: Google Docs/ VDSClass/Protocols/VINAprotocols

01/29/13- GOAL1: write/modify a Protocol and accompanying scripts so that a Freshman student could run virtual drug screening jobs with VINA on Windows Box - Christina modify -- Dr. B's original Protocol: ProtocolVINA_VDS__v5_2_WindowsBoxOnly.txt - ON GDocs folder

GOAL2: edit/make a DOS script file to sequentially dock ligands in a folder in VINA on a Windows box - Christina to make -- Dr. B's original Protocol: scriptVINAwin.bat - ON GDocs folder

GOAL3: write/modify a Protocol and accompanying scripts so that a Freshman student could run virtual drug screening jobs with VINA on DDFE - Christina to make, Alex to test

GOAL: write/modify a Protocol and accompanying scripts so that a Freshman student could run virtual drug screening jobs with VINA on TACC (Lonestar) - Alex to make, Christina to test

These should include Ligand setup, protein setup and analysis of binding scores and analysis of binding poses in a molecular graphics viewer

Some files that we can all access are stored on the DDFE /home/chem204/DatabasesVDS/Misc/VINAfilesforTACC

TASKS - figure out how to do a shared directory for us - Alex and Christina do a succesful dock of 16ligs using VINA script from Dr. B (don't do more than 50 because will get an Warnign message for too many jobs submitted) -see if Christina's vina_script030212.sh works (to concatenate .PDBQT outputs and create a Bestranking.lst) - figure out how to use 'launcher'

Dr. John Fonner at TACC says to use Launcher instead of PyLauncher for VINA on RANGER/LONESTAR

login4% module spider launcher
 * Using system spider cache file**
 * Using system spider cache file**


 * launcher: launcher/1.3**


 * Description:**
 * Utility for starting parametric job sweeps**


 * This module can be loaded directly: module load launcher/1.3**


 * Help:**
 * The launcher module file defines the environment variable:**
 * TACC_LAUNCHER_DIR for the location of the TACC Parametric**
 * Job Launcher which is a simple utility for submitting multiple**
 * serial applications simultaneously.**


 * For more information on using the Job Launcher, please consult**
 * the README.launcher file located in $TACC_LAUNCHER_DIR**


 * Version 1.3**

New **pylauncher** Utility for Packaging Serial Runs
 * TACC has released a new utility, //pylauncher//, for packaging serial runs into a parallel job. This utility is similar to the existing //launcher// module, but offers extended functionality. The existing //launcher// utility stays available, for backwards compatibility and because of its simplicity.**
 * The new //pylauncher// utility (so called because it is written in python) offers more flexibility:**
 * - improved scheduling**
 * - multiple cores per serial run**
 * - flexible job queue**
 * The //pylauncher// utility is available through the module system: module load pylauncher.**
 * The //pylauncher// module comes with a manual in $TACC_PYLAUNCHER_DIR/doc and examples scripts in $TACC_PYLAUNCHER_DIR/examples**
 * The //pylauncher// is available on lonestar, longhorn, and ranger.**
 * The //pylauncher// is available on lonestar, longhorn, and ranger.**