Docking Experiment Preparation
Setup PDB DataGrid
- Index PDB databases
- Pre-stage (all) Protein Data Bank (PDB) on replica sites
- Start PDB Server
Create Docking GridScore (receptor surface details) for a given receptor on home node.
Pre-Staging Large Files required for Docking:
- Pre-stage Dock executables and PDB access client on Grid nodes, if required (e.g., dock.Linux, dock.SunOS, dock.IRIX64, and dock.OSF1 on Linux, Sun, SGI, and Compaq machines respectively). Use globus-rcp.
- Pre-stage/Cache all data files (~3-13MB each) representing receptor details on Grid nodes.
- This can can be done demand by Nimrod/G for each job, but few input files are too large and they are required for all jobs). So, pre-staging/caching at http-cache or broker level is necessary to avoid the overhead of copying the same input files again and again!