MUD - Michael's Utilities for Docking

Revision as of 08:42, 29 October 2008 by Mysinger (talk | contribs)
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What's in MUD?

  • Tools to start, check, and restart dock jobs
  • Tools to combine, enrich, plot, and view docking results

Setting up MUD

  • For convenience, point a shell variable to the base mud directory to save typing
set mud=~mysinger/code/mud/trunk
  • If you use MUD a lot, you can add this to your ~/.login
  • Then simply run commands like this:
$mud/ -h
  • Use -h or --help to get full help information for the .py (python) scripts
  • The .csh scripts will automatically print usage information if mis-used
  • The scripts automatically use their invocation path to find other scripts and libraries they depend on.

Job Control

  • Main Workflow
  1. Submit a parallel job to the cluser

Uses 'dirlist' to determine which directories to run. Similar to startdockbksX, but also indicates job submission by touching a submitted file in each directory.

  1. Check parallel job status

$mud/ Indicates the status of unfinished (or unsubmitted) jobs. Note that it simply returns nothing if everything is finished.

  1. Restart all failed subjobs

$mud/ This works even if some subjobs are still running. Occasionally, however, jobs can fail with no detectable remnants. To force those jobs to restart you can use the -f option, but beware that this will also restart all subjobs that are still running. Other more specialized commands

  • Submit a single directory to the cluster


  • Submit a single directory to the local machine


  • Remove docking output leaving only input - will even DELETE finished jobs


  • Restart single directory


Job Analysis