CNS use case example

This use case describes how to run CNS 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 CNS script on the eNMR grid.

File: cns-example.tgz

Description of content:

This directory contains an example of structure calculation using
paramagnetic restraints in CNS (cns1.2-para) based on data provided by
Giacomo Parigi from CERM, Florence
Created by Alexandre Bonvin, Utrecht University, April 2008

run-cns.jdl: job file for grid submission, modify path as needed

run-cns: the executable script that will be run

cns-input.tgz: gzipped tar file containing all files required to run a CNS test calculation:

• Restraints files:
  • CaMM13Tmpcs1.tbl : pseudo contact shift restraints
  • CaMM13Tmrdc1.tbl : RDC restraints
  • noes.tbl : NOE restraints
  • phipsi.tbl : backbone dihedral angle restraints
  • tensor.tbl : distance restraints to attache tensor to calcium atom

• Input PDB and CNS toplogy files:
  • calmodulin-MM13.pdb
    
  • calmodulin-MM13.psf
  • tensor.pdb
  • tensor.psf

• CNS parameter files:
  • ion.param
  • par_axis.pro
  • parallhdg5.3.pro

Example structure calculation scripts:

• sa-test.inp: CNS structure calculation script

Execution on the eNMR grid (commands are in italics)

1) Login as an eNMR grid user:

voms-proxy-init -voms enmr.eu

2) Submit job file:

glite-wms-job-submit -o run-cns.jobid -a run-cns.jdl

3) Check status:

glite-wms-job-status -i run-cns.jobid

4) When finished get back output:

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