Conventional MD Replicas (AMBER)

From a PDB ID or an uploaded structure to a solvated protein–ligand system, N parallel AMBER MD replicas, per-replica analysis and a clustered HTML report.

by Temple Compute

Run Conventional MD Replicas (AMBER) on Horus

W-35 · cMD Replicas (AMBER)

From a PDB ID or an uploaded structure to a solvated protein–ligand system, N parallel AMBER MD replicas, per-replica analysis and a clustered HTML report.

Domain: Drug Discovery

Overview

Conventional MD with AMBER, from a PDB ID or uploaded structure to a solvated protein-ligand system (optional GAFF2 ligand), N parallel replicas of a 10-step equilibration plus chunked production, per-replica analysis and one clustered HTML report. The protocol is ported from MolBioMedUAB/protocols. The workflow has 10 tasks.

Pipeline

fetch_pdb            PDB ID or upload             --> structure/structure.pdb
extract_ligand       structure + residue name     --> ligand/ligand_pose.pdb
parameterize_ligand  pose                         --> ligand/ligand.mol2 + ligand/ligand.frcmod (GAFF2, AM1-BCC)
build_complex        structure + ligand           --> system/system.{prmtop,inpcrd,pdb}, system/prep_report.json
build_system         protein-only variant         (output not used downstream)
prepare_replicas     renders min/md templates     --> replicas/<i>/
equilibrate (xN) 10 steps: min, heat, restrained NPT, min, NPT, free NPT/NVT
produce     (xN) chunked production (NVT or NPT)
analyze     (xN) cpptraj: RMSD, RMSF, Rg, H-bonds, ligand RMSD/contacts
report               k-means over all replicas    --> results/report.html, results/summary.csv, results/clusters/

Inputs / Outputs

Parameters

| id | Default | Meaning | |---|---|---| | ligand_resname / ligand_chain | JZ4 / first copy | Ligand to extract | | ligand_charge | 0 | Net formal charge (AM1-BCC) | | protonate_ligand | on | Open Babel hydrogens at the pH | | chains | all | Chains to keep, e.g. A,B; hetero groups are removed | | keep_waters | off | Keep crystal waters | | protonation / ph | PROPKA / 7.0 | Protonation method (reduce = HIS tautomers only) and pH | | forcefield / water | ff14SB / TIP3P | Force field and water model | | box / padding | truncated octahedron / 12 Å | Box shape and padding | | salt_mM | 150 | NaCl on top of neutralization | | hmr | off | Hydrogen mass repartitioning (allows 4 fs) | | md_engine / amber_env | OpenMM / none | openmm or pmemd; shell line run before pmemd.cuda | | n_replicas | 3 | Independent replicas (1-20) | | temperature | 300 K | Temperature (250-400) | | length_ns / chunk_ns | 200 / 10 | Production per replica, in consecutive chunks | | timestep_fs | 0 (auto) | 4 fs with HMR, else 2 fs | | prod_ensemble | NVT | NVT or NPT | | save_every_ps | 10 | Production frame interval | | write_solvent | on | Off writes solute-only trajectories | | equil_scale / restraint_scale | 1.0 / 1.0 | Scale equilibration lengths (15 ns at 1.0) and restraint weights | | restraint_mask | auto | Solute heavy atoms, or any Amber mask | | heat_start_k, cutoff, gamma_ln, pressure_bar | 100 K, 9 Å, 3 ps⁻¹, 1 bar | Thermostat, cutoff and barostat settings | | seed | -1 | -1 random; a number derives a seed per replica and step | | analysis_stride | 1 | Analyze every Nth frame | | n_clusters | 5 | k-means clusters on backbone; 0 skips |

References