AMBER Protein MD Setup

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

by Temple Compute

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W-05 · AMBER Protein MD Setup

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

Domain: BioExcel Building Blocks

Overview

Runs AMBER (LEaP, sander, cpptraj) with ff14SB and TIP3P on a protein (default lysozyme, PDB 1AKI): topology, in vacuo minimization, solvation, NaCl, minimization, heating to 300 K, NVT and NPT equilibration, free production MD, and cpptraj analysis. The workflow has 23 tasks.

Pipeline

fetch_pdb        Download pdb_id or use the uploaded structure
pdb4amber        Prepare PDB for AMBER
gen_top          LEaP topology and coordinates (ff14SB)
sander_h_min ──► process_h_min     Minimize hydrogens in vacuo
sander_n_min ──► process_n_min     Minimize full system in vacuo
amber_to_pdb     Convert minimized structure to PDB
leap_solvate     TIP3P water box
leap_add_ions    Neutralize and add NaCl (salt_mm)
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   RMSd vs first frame, RMSd vs experiment, radius of gyration
cpptraj_image    Image trajectory, strip solvent

Inputs / Outputs

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 1AKI | RCSB PDB code; clear it to use structure | | structure | examples/1aki.pdb | Structure used when pdb_id is empty | | box_padding_a | 9.0 | Minimum solute-to-box-edge distance (A), truncated octahedron | | salt_mm | 150 | Ionic concentration on top of neutralizing ions (mM) | | 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) |

Restraints, heating protocol and cpptraj masks are set in configs/*.yaml.

References