Xplor-NIH use case

This use case describes how to run Xplor-NIH jobs on the eNMR grid.

An gzipped tar file containing all necessary files and an example of a
job file for grid submission in provided for download. This use case
provides a basis for executing any Xplor-NIH script on the eNMR grid.

File: xplor-para-example.tgz

Description of content:

This directory contains an example of structure calculation on a hemoprotein using paramagnetic restraints in XPLOR-NIH, as described in J Biomol NMR. 2004 28(3):249-246
Created by Andrea Giachetti, CIRMMP, April 2008

t_xplor.jdl: job file for grid submission, modify path as needed

run: the executable script that will be run

PARA: directory contains all input and output files

saCONV.inp: input file for XPLOR-NIH

Restraints files:

• pcshifts.tbl : pseudo contact shift restraints
• rdccouplings.tbl : RDC restraints
• noe.tbl : NOE restraints
• metalcenter.tbl : metal coordination restraints
• tensor.tbl : distance restraints to attach tensor to heme iron

Input PDB and topology files:

• protein.pdb : protein coordinates
• heme.pdb : heme group coordinates
• protein.psf : protein topology
• heme.psf : heme topology
• axis_xyzo_3_500.pdb : pcs tensor coordinates
• axis_xyzo_3_600.pdb : rdc tensor coordinates
• axis_xyzo_3_500.psf : pcs tensor topology
• axis_xyzo_3_600.psf : rdc tensor topology

XPLOR-NIH parameter files:

• ion.param
• parallhdg.hemes
• par_axis_3.pro

Execution on the eNMR grid:

1) login as an eNMR grid user:

2) submit job file:

3) check status:

4) when finished get back output:

glite-wms-job-output -i run-xplor.jobid --dir xplor-output