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RESOURCES - Computational Chemistry

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Parameterization

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  1. small molecule dihedral parameterization

Theory

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  1. Intro to Molecular Mechanics

PyMol

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  1. PyMol Wiki
  2. Advanced Scripting Tutorial

PTM DBs

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  1. Expasy
  2. Phosphosite

Task Spooler (Queuing)

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  1. ts man page

Bioexcel

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  1. BioExcel Building Blocks

Gromacs Tutorials

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  1. PTM tutorial gromcas
  2. Gromacs Analysis - NOE
  3. PlayMolecule - Protein Prepare
  4. Rizzo Lab - Tutorials for lots of different software and databases
  5. Rizzo Lab - Gromacs Instructions
  6. Analysis - Essential Dynamics - Gromacs
  7. 4 more

Quantum Chemistry

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  1. Introducing the Maple Quantum Chemistry Toolbox
  2. 11: Computational Quantum Chemistry
  3. Machine Learning Speeds Up Quantum Chemistry Calculations

Gromacs - Practical

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  1. Excellent How-to with GMX and MD
  2. Order Parameter in GMX
  3. Managing long simulations — GROMACS 2022.4 documentation

NMR Observables from MD

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  1. Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate...
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  4. Direct Simulation of Magnetic Resonance Relaxation Rates and Line Shapes from Molecular...
  5. GitHub - fahoffmann/MethylRelax: Scripts to calculate the NMR relaxation rates from pro...
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