Applications of Amber Software
Amber is a set of force fields for molecular dynamics of biomolecules, originally developed by Peter Kollman's group at the University of California, San Francisco. Amber is also the name of the molecular dynamics package that simulates these force fields. The Amber software suite provides a set of programs for applying the AMBER force field to the simulation of biomolecules. It is written in the programming languages Fortran 90 and C and supports most major Unix-like operating systems and compilers. Amber is a molecular dynamics application developed specifically for simulating biomolecular systems. To use the Amber force field, the values of the force field parameters (such as force constants, equilibrium bond lengths and angles, charges) are required. Amber supports GPU acceleration and can run explicit solvent PME and implicit solvent GB simulations. Amber runs 15 times faster on NVIDIA GPUs than CPU-only systems, allowing users to run biomolecular simulations from days to hours.
Our Services Based on Amber Software
On the Amber software platform, our scientists can provide our customers with molecular simulation, protein structure analysis, small molecule data processing, and building systems of protein-small molecule research and other comprehensive support for small molecule drug and biopharmaceutical design under a unified operating environment.
Building Systems
- Cleaning up protein PDB files for Amber
- Residue naming conventions
- Chains, residue numbering, missing residues
QM/MM Calculations
- Adaptive solvent QM/MM simulations
- Adaptive buffered force-mixing QMMM
- Semi-empirical or born-oppenheimer molecular dynamics
Constant pH Calculations
- Running at constant pH
- Analyzing constant pH simulations
- Constant pH MD replica exchange
Molecular Dynamic Simulation
Analysis of Molecular Dynamic Results
- Trajectory file observation
- Energy data mapping
- Calculate the skew variance
- Measuring the radius of gyration
- Calculate the RMSD value of the structure
- Calculate the root mean square fluctuation of atomic positions
- Calculate the number, distance or angle of hydrogen bonds between molecules during the simulation
Quantum Dynamics
- Path-integral molecular dynamics
- Centroid molecular dynamics (CMD)
- Ring polymer molecular dynamics (RPMD)
- Linearized semiclassical initial value representation
- Reactive dynamics
Our Capabilities
On the Amber software platform, our scientists can provide our customers with molecular simulation, protein structure analysis, small molecule data processing, and building systems of protein-small molecule research and other comprehensive support for small molecule drug and biopharmaceutical design under a unified operating environment.
Features of Amber Software
- Amber implements efficient simulations with periodic boundary conditions using the PME method for electrostatic interactions and the continuum model for long-range van der Waals interactions.
- Aperiodic simulations are supported using generalized Born or numerical Poisson-Boltzmann implicit solvent models.
- There is a extensive support for carbohydrate mimics, as well as proteins, nucleic acids, and small organic molecules.
- There is extensive support for trajectory analysis and energy postprocessing.
- Constraints can be very flexible and can be based on many types of NMR data.
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