Here is some documentation which may help you to run HADDOCK 2.1 on Flux. Files from the file server are also mounted there, to ease copying and moving.
Step 1: Login to flux and load the modules for haddock:
$ ssh -X uniqname@flux-login.engin.umich.edu
$ module load lsa
$ module load cns/1.2
$ module load haddock
Step 2: Move your files from the department file server to the scratch space on flux:
$ cd /dept/brd/[home/group]/[username/groupname]
example:
$ cd /dept/brd/home/bjensen
$ cp -r p450 /nobackup/bjensen/
Step 3: Move to the scratch space, and adjust the new.html file to reflect the path to your current directory. Example given below. Items to be changed are in green.
$ cd /nobackup/bjensen/p450
$ nedit new.html
<html>
<head>
<title>HADDOCK - start</title>
</head>
<body bgcolor=#ffffff>
<h2>Parameters for the start:</h2>
<BR>
<h4><!-- HADDOCK -->
HADDOCK_DIR=/home/software/rhel5/lsa/haddock2.1/<BR>
N_COMP=2<BR>
PDB_FILE1=/nobackup/bjensen/p450/testfit_1_FE3_500.pdb<BR>
PDB_FILE2=/nobackup/bjensen/p450/rec_FE3_CYF_CPH.pdb<BR>
PROJECT_DIR=/nobackup/bjensen/p450<BR>
PROT_SEGID_1=A<BR>
PROT_SEGID_2=B<BR>
RUN_NUMBER=3<BR>
UNAMBIG_TBL=/nobackup/bjensen/p450/pre_p450_b5_ NEWcuriesol_U13C15N_rem32333435_02282011.tbl<BR>
submit_save=Save updated parameters<BR>
</h4><!-- HADDOCK -->
</body>
</html>
Now run haddock to setup the run:
$ haddock
Step 4: Modify anything in the run folder that needs to be changed. Examples:
- files in protocols
- files in toppar
- others
Step 5: Copy the haddock tools to the run directory:
$ cd /nobackup/bjensen/p450/run3/
$ cp /home/software/rhel5/lsa/haddock2.1/haddock_setup.tgz .
$ tar -xvf haddock_setup.tgz
Step 6: Modify the following line in the haddock.pbs file to reflect the amount of time it will take for the entire caluclation to take. Change walltime to reflect hh:mm:ss. Guidelines:
- 500: ~6-8 hours
- 1000: ~14-18 hours
- 2000: ~36-48 hours
#!/bin/csh
#PBS -N haddock
#PBS -l nodes=1:ppn=1,
walltime=16:00:00,qos=biophysics_flux
#PBS -M
uniqname@umich.edu
#PBS -m abe
#PBS -q flux
#PBS -j oe
#PBS -V
#PBS -A biophysics_flux
#PBS -o haddock.out
#PBS -e haddock.err
Step 7: Modify the run.cns to setup your experiment also make sure to include the proper paths to the run (e.g. /nobackup/bjense/p450/run3).
Step 8: Execute the job:
$ qsub haddock.pbs
and
$ qstat -uuniqname
to check the status
