3D DOCK

Category

Computational Chemistry

Program On

pcluster

Version

2.0

Author / Distributor

See 3D Dock

Description

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

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

Documentation

-User manual available in /usr/local/3D_Dock/docs/

-More information at 3D Dock

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

64-bit Linux