About Course
💻 3-Day Hands-On Workshop | 🕒 1–1.5 Hours/Day
Course Content
Day 1: Introduction & System Preparation
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Overview of Schrödinger Suite & Desmond
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Installing & launching Maestro (GUI intro)
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Protein Preparation Wizard:
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Importing structure (PDB)
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Preprocessing, assigning bond orders, adding hydrogens
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Removing waters, fixing missing residues
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Removing waters, fixing missing residues
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Ligand preparation (LigPrep basics)
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Building the system: Solvation, box type, ions, force fields
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Practice: Prepare a protein-ligand complex for simulation
Day 2: Running Molecular Dynamics in Desmond
Day 3: Trajectory Analysis & Interpretation
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