GROMACS Protein-Ligand Complex MD Setup

Set up and run GROMACS MD of a protein-ligand complex from a PDB entry or an uploaded structure.

by Temple Compute

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W-09 · GROMACS Protein-Ligand Complex MD Setup

Set up and run GROMACS MD of a protein-ligand complex from a PDB entry or an uploaded structure.

Domain: BioExcel Building Blocks

Overview

Runs GROMACS on a protein-ligand complex (default T4 lysozyme L99A/M102Q with 2-propylphenol, PDB 3HTB, ligand JZ4). The structure is split into protein (AMBER99SB-ILDN) and ligand (GAFF via ACPype), merged into a restrained complex, solvated, ionized, minimized, equilibrated, and run as free MD with analysis. The workflow has 35 tasks.

Pipeline

fetch_pdb              Download pdb_id or use the uploaded complex
Ligand branch:
extract_heteroatoms ──► reduce_add_hydrogens ──► babel_minimize ──► acpype_params_gmx
make_ndx_ligand ──► genrestr          Ligand position restraints
Protein branch:
extract_molecule ──► fix_side_chain ──► pdb2gmx
Merge:
trjconv_protein, trjconv_ligand ──► cat_pdb_complex ──► append_ligand
editconf               Truncated octahedron box
solvate                SPC water
grompp_ions ──► genion               Neutralizing NaCl
grompp_minimize ──► mdrun_minimize ──► gmx_energy_min
make_ndx_complex       Complex index groups
grompp_nvt ──► mdrun_nvt ──► gmx_energy_nvt
grompp_npt ──► mdrun_npt ──► gmx_energy_npt
grompp_free ──► mdrun_free           Free production MD
gmx_rms_first / gmx_rms_exp / gmx_rgyr   RMSd and radius of gyration
gmx_image ──► gmx_trjconv_str_dry    Re-center, extract dry structure

Inputs / Outputs

Input: pdb_id (RCSB code) or, when empty, the structure upload; the ligand is extracted by ligand_code.
Outputs (results/): downloaded.pdb, ligand.pdb, protein.pdb, fixed.pdb, pdb2gmx.gro, ligand.params.{gro,itp,top}, ligand_posres.itp, complex_H.pdb, ionized.gro, min_energy.xvg, nvt_temp.xvg, npt_PD.xvg, md.gro, md.trr, rms_first.xvg, rms_exp.xvg, rgyr.xvg, dry.gro.

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 3HTB | RCSB PDB code; clear it to use structure | | structure | examples/3htb.pdb | Complex used when pdb_id is empty; ligand must be HETATM records named ligand_code | | ligand_code | JZ4 | Ligand residue name; selects, parameterizes and restrains the ligand | | ligand_charge | 0 | Formal net charge of the ligand, passed to ACPype | | equilibration_steps | 5000 | Steps per restrained equilibration stage (2 fs/step) | | production_steps | 25000 | Steps of the free production run (2 fs/step) |

Force field, box, ions and restraints are set in configs/*.yaml.