3D_DOCK

Category(ies): Computational Chemistry

Version: 2.0

Author / Distributor: See http://www.bmm.icnet.uk/docking/

Description:

A suite of protein docking programs, including FTDock and RPScore (MultiDock is not available here).

altix: not available on altix

inQuiry: not available at inQuiry

pcluster: Running Program | Documentation | Installation | System

Running Program:

Example: Shell script to run one of the sample files provided in /usr/local/3D_Dock/tutorial:

To run a serial job (serial.sh):

#!/bin/csh
cd working_directory
/usr/local/3D_Dock/scripts/preprocess-pdb.perl -pdb 1FTL.pdb
/usr/local/3D_Dock/bin/ftdock -static 2pka.parsed -mobile 5pti.parsed

To submit a 10 hour long serial job to the batch queue:

pcluster> ugsub T1-i1-t1-10h serial.sh

Type llqueue at your pcluster login prompt to get more information about the batch queuenames.

Documentation:

User manual available in /usr/local/3D_Dock/docs/
More information at http://www.bmm.icnet.uk/docking/

Installation:

Installed in /usr/local/3D_Dock/
PDB files preprocessing perl scripts installed in /usr/local/3D_Dock/scripts.
The executables in /usr/local/3D_Dock/bin are for serial jobs.

System: Unix (AIX)

rcluster,IOB: not available on rcluster, IOB