AMBER Protein-Ligand Complex MD Setup

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

by Temple Compute

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W-15 · AMBER Protein-Ligand Complex MD Setup

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

Domain: BioExcel Building Blocks

Overview

Runs AmberTools on a protein-ligand complex (default T4 lysozyme L99A/M102Q with 2-propylphenol, PDB 3HTB, ligand JZ4): GAFF ligand parameters via ACPype, a combined LEaP topology, minimization, solvation, ions, heating, NVT/NPT equilibration, sander production MD, and cpptraj analysis. Residues listed in remove_ligands (by default the 3HTB crystallization additives) are stripped before pdb4amber; names absent from the structure are ignored. The workflow has 29 tasks.

Pipeline

fetch_pdb              Download pdb_id or use the uploaded complex
remove_pdb_water ──► remove_residues ──► pdb4amber   Protein branch
extract_heteroatoms ──► reduce_add_hydrogens ──► babel_minimize ──► acpype_params_ac   Ligand branch
leap_gen_top           Complex topology
sander_h_min ──► process_h_min     Minimize ligand hydrogens in vacuo
sander_n_min ──► process_n_min     Minimize full system in vacuo
amber_to_pdb           Convert to PDB
leap_solvate           Truncated octahedron water box
leap_add_ions          Neutralize and add ions
sander_min ──► process_min         Minimize solvated system
sander_heat ──► process_heat       Heat 0 to 300 K
sander_nvt ──► process_nvt         NVT equilibration
sander_npt ──► process_npt         NPT equilibration
sander_free            Free production MD
cpptraj_rms_first / cpptraj_rms_exp / cpptraj_rgyr / cpptraj_image   RMSd, radius of gyration, imaging

Inputs / Outputs

Input: pdb_id (RCSB code) or, when empty, the structure upload; the ligand is selected by ligand_code.
Outputs (results/): complex.pdb, complex.stripped.pdb, ligand.pdb, ligand.reduce.H.pdb, ligand.H.min.mol2, ligand_params.{inpcrd,frcmod,lib,prmtop}, structure.leap.{pdb,top,crd}, structure.ions.{pdb,parmtop,crd}, sander.free.netcdf, complex_rms_first.dat, complex_rms_exp.dat, complex_rgyr.dat, complex_imaged_traj.trr.

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; extracted, parameterized and restrained in vacuo | | remove_ligands | PO4,BME | Comma-separated residue names stripped from the complex before pdb4amber; empty removes none | | ligand_charge | 0 | Formal net charge of the ligand, passed to ACPype | | equilibration_steps | 500 | sander steps per restrained equilibration stage (2 fs/step) | | production_steps | 2500 | sander steps of the free production run (2 fs/step) | | ionic_concentration_mm | 150 | Na+/Cl- salt concentration (mM) added by LEaP on top of neutralisation |

Force fields, restraints and thermostat are set in configs/*.yaml.