XPLOR-NIH

Category(ies): Computational Chemistry

Author / Distributor: Authors of the NIH extensions to X-PLOR: G. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandra. When publishing work which utilizes Xplor-NIH, please cite:

C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore, The Xplor-NIH NMR Molecular Structure Determination Package, J. Magn. Res., 160, 66-74 (2003).

A list of other relevant references can be found on the XPLOR-NIH website.

Description:

XPLOR-NIH is a macromolecule structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH.

altix: not available on altix

inQuiry: not available at inQuiry

pcluster: not available on pcluster

rcluster,IOB: Running Program | Documentation | Installation | System

Running Program:

To run XPLOR-NIH interactively, start the application as follows:

rcluster> xplor

If you are planning to run XPLOR-NIH interactively for more than 10 minutes, please run it on an interactive node instead of the rcluster headnode.

XPLOR-NIH can also be run on the batch queue. Here are examples of how this can be done:

1. A sample serial job:

Sample job submission shell script file sub.sh to run XPLOR-NIH in the batch queue using one processor:

#!/bin/csh
cd working_directory
xplor < test.inp > test.out

2. A sample parallel job:

Sample job submission shell script file sub.sh to run a batch parallel XPLOR-NIH job (in this example the software is used with the -tcl option):

#!/bin/csh
cd working_directory
echo $LSB_HOSTS
cat /dev/null > mlist.$$
foreach variable ($LSB_HOSTS)
   echo $variable >> mlist.$$ 
end
xplor -parallel -machines ./mlist.$$ -tcl input.tcl
rm -f mlist.$$

For information on how to submit serial or parallel jobs to the batch queue, please refer to Running Jobs on rcluster.

Documentation:

Sample input files are available in /usr/local/xplor-nih-2.15.0/eginput/
Files for the tutorial are available in /usr/local/xplor-nih-2.15.0/tutorial/
User manual and other documentation are available on the XPLOR-NIH website.

Installation:

Installed in /usr/local/xplor-nih-2.15.0/
There is a symbolic link to the xplor script in /usr/local/bin, a directory that is in the default path for all users.

System: 64-bit Linux