MD Simulation Procedure: Protein Preparation, Solvation, Minimization
Explore the basic steps for molecular dynamics (MD) simulations, including protein preparation, solvation, ionization, minimization, and MD simulation. Learn about downloading, extracting, and fixing protein structures, protonation states, solvating, ionizing systems, and parameterizing small molecules for simulations. Discover configuration files, interactions, and control parameters for accurate MD simulations.
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Presentation Transcript
Basic procedure for MD simulations Yaozong Li Nov. 20, 2017 1
Protein preparation 1 Solvating the system Ionizing 2 Minimization 3 4 MD simulation 2
1. Protein preparation 1. Download original PDB file (1p4o, chain A) 2. Extract the target structure 3. Fix the structure (check the sequence, add hydrogen, regulate side chains of protein residues, make up the missing parts) IGF-1RK Apo (PyMoL Show) Chem. Sci., 2017, 8, 3453 3464 3
Protonation states rotation 4
2. Solvating and ionizing the system (PyMoL Show) 5
3 & 4. Minimization & MD simulation Configuration file: 1. Structure (psf) 2. Coordinates (PDB) 3. Parameters 4. Interactions (vdW & electrostatic) 5. Temperature & pressure control 6. Periodic boundary conditions 6
5. Parameterization of small molecules An easy way: search parameter databases (e.g., https://cgenff.paramchem.org/) 7
Example J Comput Chem. 2010 Mar;31(4):671-90. 8
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