DOCK 3.7 2016/09/16 abl1 Tutorial(building)

This tutorial uses the DOCK-3.7-beta3. This is a supplemental tutorial for DOCK 3.7 2015/04/15 abl1 Tutorial. Former one works well and is very simple and clear. This tutorial mentions some updates in job submissions.

This is for a Linux environment and the scripts assume that you are running on SGE queueing system.

Submit an enrichment calculation via new 0003.lig-decoy_enrichment.csh

• Go to the working directory of your account

cd /nfs/home/$USERNAME/work/DOCK_tutorial

PS: $USERNAME is your username log on the cluster.

The hierarchy of the working directory:

DOCK_tutorial ----- 2HYY ------ dockfiles
              |          |
              |          |----- working
              |          |
              |          ------ other files generated by 0001.be_balsti_py.csh
              |
              ----- databases ------ decoys
                              |
                              |----- ligands
                              |
                              ------ ligands.ism and decoys.ism files

Submit

• There are two ways to get databases:

1. get databases via the script autodude_db_download.py in the DOCK 3.7