Post on 27-Mar-2015
The Avian Flu Grid Project
Rommie Amaro & Dong Xu
University of California, San Diego
PRAGMA 13 - NCSA
Sept 25, 2007
Outline
• Meet the Team• Project goals & motivation• Overall scheme• Running jobs on the PRAGMA grid• Analyze the results w/ AutoDockTools
Meet the Avian Flu Team
Neuraminidase as Drug Target
Developed against N9
sialic acid DANA zanamivir (Relenza)
Oseltamivir (Tamiflu)
Clercq, Nat Rev. Drug Disc.,5: 1015-1025 (2006)Moscana, New Eng. J. Med., 353: 1363-1373 (2006)
Group 1 and 2 Neuraminidases
Russell et al, Nature, 443: 45-49 (2006).
Relaxed Complex Method
Cluster
Cluster
Cluster
Autodock
NAMDOther
Resource
12 CPUs
Autodock
BLAST
Other Resource
64 CPUs
NAMD
Autodock 8 CPUs
Other Resource
CSF4 Meta-Scheduler
Available Resource Lists
Resource
Scheduling Modules
Resource Requirements
Autodock1990 CPUs
NAMD24 CPUs
Autodock100 CPUs
Autodock1 CPU
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User
Grid Job Submission
Demo
• Submit docking jobs on grid
• Analyze results with AutoDockTools
Molecular Dynamics Simulations
• Start with the crystal structure• Ligands (tamiflu), ions• Explicit solvent, 0.15M NaCl• 112,457 atoms
• NAMD2, Amber99 force field• 2 fs timestep, PBC, PME• SDSC Datastar Benchmark: 112
processors, 0.21 days/ns need fast interconnect between processors - not for grid
• Data: tens - hundreds of GB