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Protein Preparation

StemSkills Lab > Protein Preparation
How to Generate a GROMACS Topology with pdb2gmx: A Step-by-Step Beginner’s Guide
02
Aug

Learn to run gmx pdb2gmx step by step, pick a force field and water model, and fix the “residue not found” error before your first MD run.

Posted in: Molecular Modeling ,
Tags: Computational Biology , Force Fields , GROMACS , Molecular Dynamics , pdb2gmx , Protein Preparation ,
How to Prepare a Protein Structure for MD Simulation (Missing Residues, Hydrogens, Protonation)
10
Jul

Learn to clean a raw PDB for MD: rebuild missing loops, add hydrogens, and fix His, Asp and Cys protonation so your simulation does not crash.

Posted in: Molecular Modeling ,
Tags: GROMACS , Molecular Dynamics , PROPKA , Protein Preparation , Protonation States , Structural Bioinformatics ,