.. hightlight:: rst

Pdb2pqr Roll

Contents

• Pdb2pqr Roll
  • Introduction
  • Requirements
  • Building
    • Installing
  • What is installed

Introduction

This roll installs pdb2pqr - Poisson-Boltzmann electrostatics calculations software plus precompid apbs libraries ./pdb2pka/_apbslib.so

Requirements

Download networkx

https://pypi.python.org/packages/source/n/networkx/networkx-1.10.tar.gz
https://pypi.python.org/packages/source/d/decorator/decorator-4.0.4.tar.gz

Execute bootstrap.sh to create v.20.0.0 distro tar.gz file. pdb2pqr-2.0.0.tar.gz

Building

To build the roll execute:

# make roll 2>&1 | tee build.log

Installing

1. A roll can be added during a frontend build as any other roll.

2. A roll can be added to the existing frontend. Execute all commands from roll top level directory

   # rocks add roll *.iso
   # rocks enable roll pdb2pqr
   # (cd /export/rocks/install; rocks create distro)
   # rocks run roll pdb2pqr > add-roll.sh
   # bash add-roll.sh 2>&1 | tee install.log
   

What is installed

On opal-server node:

/etc/httpd/conf.d/pdb2pqr.conf
/opt/opal/deployed/pdb2pqr_*.xml (2 versions)
/var/www/html/pdb2pqr/index.html (redirect to current version X)
ln -s /share/opal/pdb2pqr/tmp /opt/pdb2pqr_X/tmp (for each version X)

On opal-server and compute nodes:

/etc/cron.daily/pdb2pqr-job-cleanup
/etc/profile.d/pdb2pqr.csh
/etc/profile.d/pdb2pqr.sh