Use AMBER Relaxation
Official Neurosnap webserver for accessing AMBER Relaxation online.
Overview
Relax a protein structure using an AlphaFold2 and OpenMM implementation of an AMBER forcefield.
Neurosnap Overview
The AMBER Relaxation online webserver allows anybody with a Neurosnap account to run and access AMBER Relaxation, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
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.
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API Request
Access AMBER Relaxation using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Inputs & Configuration
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