PELE 1.8 documentation

Contents:

• Installation
  • PELE++
  • PelePlatform
• Introduction
  • Software
  • Simulation
  • Basic Analysis
• Tutorial
  • RoRγ: Dissociation Pathway to guide unbiased binding simulation
  • Hemagglutinin: Pocket Detection
  • MgluR5: Pose Prediction on GPCRs
  • Progesteron Receptor
• Launch your first job
• PELE Theory
  • Overview
  • Energy Function
• PELE Molecular Parameters
  • Solvent parameters
  • Template parameters
  • Hetero group rotamer library files
  • Conformation library files
• PelePlatform
• Adaptive PELE
• Frag PELE
• MSM PELE
• Pele Output
  • Report file
  • Trajectory file
  • Steps folder
• Reference Manual
  • General Structure of a control file in Pele++
  • Initialization Block in Pele++ control file
  • PELESimulation command
  • Conditions in Pele++ control file
  • Selections By Example
  • How to run PELE in multicore platforms
  • PCA for the perturbation phase of PELE
  • Real Time Control of PELE simulations (experimental)
  • PELE File Formats
  • PELE default parameters
  • PELE Error Messages
• How to contribute to the documentation
  • Notes on writing a page of documentation
• References
• Release notes
  • Version 1.9.0
  • Version 1.8.1
  • Version 1.8.0
  • Version 1.7.1
  • Version 1.7
  • Version 1.6.1
  • Version 1.6
  • rev12510
  • rev12489
  • rev12455
  • rev12360
  • rev12308
  • rev12183
  • rev12025
  • rev11996
  • rev11893
  • rev11678
  • rev11670
  • rev11620
  • rev11368
  • rev11362
  • rev11335
  • rev11260
  • rev11227
  • rev11145
  • rev11122
  • rev11056

License

Copyright 2010-2024 BARCELONA SUPERCOMPUTING CENTER.

(see below for the text in English)

Software desarrollado por el grupo “Electronic and Atomic Protein Modelling”.

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Software developed by the Electronic and Atomic Protein Modelling group.

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