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
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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
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New pylauncher Utility for Packaging Serial Runs
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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.
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