3D DOCK: Difference between revisions
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[[Category:Zcluster]][[Category:Computational Chemistry]][[Category:Bioinformatics]] | |||
[[Category:Zcluster]][[Category: | |||
=== Category === | === Category === | ||
=== Program | Bioinformatics | ||
=== Program On === | |||
pcluster | pcluster | ||
=== Version === | === Version === | ||
2.0 | |||
2.0 | |||
=== Author / Distributor === | === Author / Distributor === | ||
See [http://www.bmm.icnet.uk/docking/] | |||
=== Description === | === Description === | ||
A suite of protein docking programs, including FTDock and RPScore (MultiDock is not available here). | |||
=== Running Program === | === 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 === | === Documentation === | ||
-User manual available in /usr/local/3D_Dock/docs/ | |||
-More information at [http://www.bmm.icnet.uk/docking/] | |||
=== Installation === | === 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 === | === System === | ||
64-bit Linux | Unix (AIX)?! [64-bit Linux] | ||
Revision as of 09:39, 5 February 2013
Category
Bioinformatics
Program On
pcluster
Version
2.0
Author / Distributor
See [1]
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 [2]
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]