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Scripting Workflows with the Application Hosting Environment

Learn how to construct complex workflows using the Application Hosting Environment (AHE) to automate job preparation, simulation starts, monitoring, output retrieval, and job chaining. Explore a workflow example involving HIV-1 Protease Monomer B and discover the process of Structure-Assisted Drug Design with FDA inhibitors. Dive into computational techniques like Ensemble MD suited for HPC GRID, enabling conformational sampling through simultaneous runs and equilibration protocols. Use Perl scripting to automate job processes, distribute tasks, and chain jobs effectively.

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Scripting Workflows with the Application Hosting Environment

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  1. Scripting Workflows with the Application Hosting Environment Stefan Zasada University College London

  2. Constructing workflows with the AHE • By calling command line clients from Perl script complex workflows can be achieved • Easily create chained or ensemble simulations • For example jobs can be chained together: • ahe-prepare  prepare a new simulation for the first step • ahe-start  start the step • ahe-monitor  poll until step complete • ahe-getoutput  download output files • repeat for next step

  3. Constructing a workflow ahe-prepare ahe-start ahe-monitor ahe-getoutput

  4. HIV-1 Protease Monomer B 101 - 199 Monomer A 1 - 99 • Enzyme of HIV responsible for protein maturation • Flexible Flaps open to provide access to active site1 • Catalytic Asp Dyad cleaves peptide bond • Example of Structure Assisted Drug Design – 8 FDA inhibitors Flaps Glycine - 48, 148 Saquinavir RMSD of existing crystal structures2 P2 Subsite Catalytic Aspartic Acids - 25, 125 C-terminal N-terminal Leucine - 90, 190 • Hornak et al., PNAS, 2006, 103 4, 915-920 • Zoete et al., J. Mol. Biol., 2002, 315, 21-52

  5. Computational Techniques Ensemble MD is suited for HPC GRID • Simulate each system many times from same starting position • Each run has randomized atomic energies fitting a certain temperature • Allows conformational sampling End Conformations Start Conformation Series of Runs Launch simultaneous runs (60 sims, each 1.5 ns) C1 C2 Cx C3 Equilibration Protocols C4 eq1 eq2 eq3 eq4 eq5 eq6 eq7 eq8

  6. Files MD Applications Processes VMD • Strip out relevant pdb information • Incorporate mutations • Ionize and solvate to build system • Static Equilibration files are built according to variable protocol; output feeds into input of next equilibration • Each step of the chained equilibration protocol runs sequentially • End equilibration output serves as input of the production run • Production run • Output files of simulation are used as input for analysis • Analysis returns files containing required data for end user Protein Data Bank 1 Initialization 2 Starting Structure Files 3 AMBER 4 Eq 0 Eq 1 5 Eq 2 Eq 3 Equilibration protocol … NAMD Eq n 7 6 Simulation start files Production Phase … Output files 8 Analysis Input 9 Analysis CHARMM Analysis Output Simulation Workflow

  7. Practical 2 Using Perl: • Write script to automate preparing and starting a job, and staging files • Write script to distribute jobs around a number of resources • Write script to chain jobs, one after the other http://www.realitygrid.org/AHE/training/brunel/ex2/

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