AMBER Relaxation
Relax a protein structure using an AMBER settling protocol.
Relax a protein structure using an AlphaFold2 and OpenMM implementation of an AMBER forcefield.
Estimated resource cost: 0.000527
Categories: Molecular Dynamics & Simulation
Tags: Energy Minimization Molecular Dynamics Structure Fixing
Key Capabilities
- 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
Runtime Statistics
| Metric | Value |
|---|---|
| runtime_mean | 36 |
| runtime_median | 14 |
| runtime_std | 121 |
| runtime_90th_percentile | 60 |
| runtime_max | 2702 |
Similar Tools
- GROMACS Molecular Dynamics
- gmx_MMPBSA
- AlphaFlow
- BindFilter
Ready to submit your job?
Review your configuration, then confirm the estimated credit cost before you run the job. Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: 0.000527
Invite-only, limited-time access. Please contact ztang@getantibody.com.
Invite-only, limited-time access. Please contact ztang@getantibody.com.