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Run eHiTS (the ligand docking software) on clusters

Intro: eHiTS is a fast ligand docking program and it has been successfully installed on the HPres cluster. Detailed information can be viewed from the eHits website.

Before you go further, please make sure your working environment has been setup correctly -- especially the passwordless connection in the cluster!


Step 1: Copy the following ehits job script into your own home directory, create a job script file called ehits.lsf

#!/bin/bash

# enable your environment, which will use .bashrc configuration in your home directory
#BSUB -L /bin/bash

# the name of your job showing on the queue system
#BSUB -J ehits

# the queue that you will use, the example here use the queue called "normal"
# you might want to use "long" queue if you have a very large library
# please use bqueus command to check the available queues
#BSUB -q normal


# the system output and error message output, %J will show as your jobID
#BSUB -o %J.out
#BSUB -e %J.err


#when job finish that you will get email notification
#BSUB -u yourID@partners.org
#BSUB -N


#enter your working directory
cd /shr/home/$USER/



#the following command is adopted from eHits mannual, the argument "-lsf_node 10" is to allocate 10 nodes
#to dock the complex against the ligand library you shall be able to use other commands supplied
# by eHits manual as well and please change the path info to your complex or your ligand library file.
# DO NOT change the path to the ehit.sh

/source/eHits_6.2/ehits.sh -lsf_nodes 10 -complex /path/to/your/pdbfile/example.pdb -ligand /path/to/your/library/example.sdf

[testy@n137 ~]$ bsub < ehits.lsf

[testy@n137 ~]$ bjobs
[testy@n137 ~]$ bjobs
JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
880761  testy   RUN   normal     n62         lsfhost.loc ehits      Sep 18 15:31
880762  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880763  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880764  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880765  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880766  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880767  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880768  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880769  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880770  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32
880771  testy   RUN   normal     n37         lsfhost.loc eHiTS      Sep 18 15:32

[testy@n137 ~]$ cd ehits_work/
[testy@n137 ehits_work]$ ls
license  logs  preprocess  results
[testy@n62 ehits_work]$ ls -lt
total 16
drwxrwxr-x  4 testy testy 104 Sep 18 15:45 logs
drwxrwxr-x  3 testy testy 104 Sep 18 15:45 results
drwxrwxr-x  4 testy testy 104 Sep 18 15:32 preprocess
drwxrwxr-x  2 testy testy 248 Sep 18 15:32 license