Use AMBER Relaxation

Features

• Uses OpenMM for molecular dynamics-based energy minimization
• Implements Amber14 force field with TIP3P water model
• Removes water molecules and non-biopolymers before minimization
• Fixes missing residues, atoms, and hydrogen placements using PDBFixer
• Clamps energy minimization tolerance between 0.1 and 10.0 Kcal/mol
• Converts tolerance from Kcal/mol to kJ/mol for OpenMM compatibility
• Uses Langevin integrator with a 2 fs time step at 300K
• Computes initial and final potential energy values in kJ/mol
• Computes RMSD between original and minimized structure in Ångströms
• Saves the minimized structure in PDB format
• Logs energy minimization progress and outputs results in JSON format
• Allows customization of maximum iterations and minimization tolerance
• Uses OpenMM’s NoCutoff method for non-bonded interactions
• Applies hydrogen bond constraints for improved stability
• Perfect for quickly fixing side chains and other minor stereochemical issues from models like AlphaFold

Statistics

Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.