XPLOR-NIH is a structure determination program which builds on the X-PLOR v 3.851 program, including additional tools developed at the NIH. These tools include functionality for the following:
- 3J couplings
- 1J couplings
- 13C shifts
- 1H shifts
- dipolar couplings
- radius of gyration
- conformational database torsion angle potentials
- database base-base positioning potentials for DNA
- interface to the NMR graphics package VMD-XPLOR, downloadable separately.
- embedded Python and TCL interpreters.
The advantage of running Xplor-NIH on Biowulf would be to spawn a large number of independent refinement jobs which would run on multiple Biowulf nodes. Note that each run is not parallel; the speedup is produced by the swarm of independent jobs. Thus it is ideally suited for refining multiple NMR structure models. Xplor-NIH is based on Xplor 3.851.
XPLOR was developed at Yale University, and the NIH extensions were developed by G. Marius Clore, John Kuszewski, Charles D. Schwieters, and Nico Tjandra at the NIH.
Running Xplor-NIH on Biowulf
To set up the paths for Xplor-NIH, use 'module load xplor-nih'. This will load the default (latest) version of Xplor-NIH. To load a particular version, use the module commands as demonstrated below:
[user@biowulf ~]$ module avail xplor-nih ------------------------ /usr/local/Modules/3.2.9/modulefiles -------------------- xplor-nih/2.31 xplor-nih/2.32 [user@biowulf ~]$ module load xplor-nih/2.31 [user@biowulf ~]$ module list Currently Loaded Modulefiles: 1) xplor-nih/2.31
Xplor-NIH requires the usual set of Xplor input files -- coordinates, xplor input files, topology/parameter files. The 'standard' files are in /usr/local/xplor-nih/.
To submit an Xplor-NIH batch job on Biowulf, you need a PBS batch
Sample script, modified from Charles Schwieters.
#/bin/sh # # This is a PBS script to run parallel XPLOR-NIH jobs on Biowulf # CDS - 12/16/02 # # # PBS stuff # #PBS -N xplor-nih #PBS -S /bin/sh #PBS -m be #PBS -k oe # # cd to the 'working' directory, from where the job is being submitted. # This can also be set to an explicit pathname. # cd $PBS_O_WORKDIR # # uncomment if the script is a python script # #PY=-py # # name of XPLOR script # XPLOR_SCRIPT=test.inp # # name of output file (output will appear in script.out.#) # where # is 0-(num processors) # LOGFILE=script.out # #location of xplor # module load xplor-nih # #list of nodes on which to run: # this to run two jobs on each node. Do not change this. # XPLOR_MACHINES=xplor_machines.$PBS_JOBCOOKIE cat $PBS_NODEFILE $PBS_NODEFILE > $XPLOR_MACHINES # # run xplor # env XPLOR_RSH="rsh -n" \ xplor $PY -parallel -o $LOGFILE -machines $XPLOR_MACHINES \ < $XPLOR_SCRIPT # # clean up # rm $XPLOR_MACHINES
Submit this job with a command like:
qsub -l nodes=8 scriptname
Monitoring your job
\As with all jobs on Biowulf, the individual job or the entire system can be monitored with a variety of web-based tools. On the right is an image of the monitor for all jobs belonging to one user. See the Biowulf user guide for a description of these tools.
BenchmarksXplor-NIH test suite.
12 x 2.8 GHz Intel X5660
8 x 2.67 GHz Intel X5550