Protein Preparation, Ligand Parameterization & Topology Generation for GROMACS

By BioDockify Computational Research Team · August 8, 2026 · GROMACS Workflow

How to prepare protein structures and parameterize ligands for GROMACS molecular dynamics. Covers pdb2gmx, GAFF parameterization with acpype, and topology merging for protein-ligand complexes.

Read the complete article with tables, code and references on BioDockify.

Key References

• Abraham, M.J. et al. GROMACS. SoftwareX 1-2, 19-25 (2015).
• Sousa da Silva, A.W. & Vranken, W.F. ACPYPE - AnteChamber PYthon Parser interfacE. BMC Res Notes 5, 367 (2012).
• Wang, J. et al. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph. Model. 25, 247-260 (2006).

Scope & Limitations

GAFF parameterization requires antechamber/acpype installed Unusual ligands may fail automatic parameterization Missing residues need manual modeling before pdb2gmx