View source for 3D DOCK

[[Category:Zcluster]][[Category:Software]][[Category:Computational Chemistry]]  
=== Category ===

Bioinformatics

=== Program On ===

pcluster

=== 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).

=== 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):
<pre class="gscript">
#!/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
</pre> 

To submit a 10 hour long serial job to the batch queue:
<pre  class="gcommand">
 pcluster> ugsub T1-i1-t1-10h serial.sh
</pre>


=== 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)?! [64-bit Linux]