AMBER Constant-pH MD Setup

Predict per-residue pKa values with constant-pH MD in AMBER.

by Temple Compute

W-16 · AMBER Constant-pH MD Setup

Predict per-residue pKa values with constant-pH MD in AMBER.

Domain: BioExcel Building Blocks

Overview

Runs constant-pH MD with AmberTools on a protein (default BPTI, PDB 6PTI): ff14SB with constph templates, truncated octahedron TIP3P box, ions, a cpinutil input for the chosen titratable residues, heat/NVT/NPT equilibration, constant-pH production with sander, and protonation analysis with cphstats. The workflow has 16 tasks.

Pipeline

fetch_pdb          Download pdb_id or use the uploaded structure
pdb4amber          Prepare structure for constant-pH AMBER
leap_gen_top       Topology (ff14SB + constph)
leap_solvate       Truncated octahedron TIP3P box
leap_add_ions      Neutralize and add ions
parmed_cpinutil    Constant-pH input for titratable residues
sander_min ──► process_min     Minimize with backbone restraints
sander_heat ──► process_heat   Heat 0 to 300 K
sander_nvt ──► process_nvt     NVT equilibration
sander_npt ──► process_npt     NPT equilibration
sander_cph_free    Constant-pH production MD (solvph = solvent_ph)
cphstats           Protonation states and pKa

Inputs / Outputs

Input: pdb_id (RCSB code) or, when empty, the structure upload.
Outputs (results/): structure.pdb, structure.pdb4amber.pdb, structure.leap.{pdb,top,crd}, structure.ions.{pdb,parmtop,crd}, structure.cpin, structure.cpH.parmtop, sander.pH.{netcdf,rst,cpout,cprst,log,mdinfo}, cphstats.pH.dat, cphstats.pH.pop.dat.

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 6PTI | RCSB PDB code; clear it to use structure | | structure | examples/6pti.pdb | Protein used when pdb_id is empty | | solvent_ph | 7.0 | Solvent pH of the constant-pH Monte Carlo moves (solvph) | | titratable_residues | AS4, GL4, CYS, LYS, TYR | Residue types allowed to change protonation (also HIP) | | salt_m | 0.1 | Ionic strength for generalized-Born protonation energies (saltcon, M) | | production_steps | 2500 | sander steps of the production run (2 fs/step; moves every 100 steps) |