AMBER

AMBER is used to minimize the bond stretching energy of this ethane molecule.

Family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman's group at the University of California, San Francisco.

- AMBER

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Peter Kollman

Professor of chemistry and pharmaceutical chemistry at the University of California, San Francisco.

Albert Einstein as a professor

He is known for his work in computational chemistry, molecular modeling and bioinformatics, especially for his role in the development of the AMBER force field and molecular dynamics software package.

University of California, San Francisco

Public land-grant research university in San Francisco, California.

Toland Hall in 1887. Toland Hall on Stockton was the first home of the school, before its transfer to the Parnassus campus.
The Affiliated Colleges buildings in 1908, with the streetcar that used to run on Parnassus
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The Mission Bay Campus, UCSF's second campus, developed starting in 1999
The Institute for Regeneration Medicine, designed by Rafael Viñoly and completed in 2010
The Parnassus campus, home of many academic programs and the UCSF Medical Center, with Mount Sutro and the Sutro Tower in the background
The Mission Bay campus, with Genentech Hall and the Rutter Community Center facing Koret Quad
Benny Bufano's Bear and Cub sculpture outside Kalmanovitz Library
Buildings at the Mission Bay campus
UCSF Fresno
The Rutter Community Center, which serves as the hub of student life in the Mission Bay campus

Peter Kollman – developer of the AMBER force field in molecular dynamics simulation and an internationally renowned computational chemist

Force field (chemistry)

Computational method that is used to estimate the forces between atoms within molecules and also between molecules.

A force field is used to minimize the bond stretching energy of this ethane molecule.
Molecular mechanics potential energy function with continuum solvent.

AMBER, CHARMM, and GROMOS have been developed mainly for molecular dynamics of macromolecules, although they are also commonly used for energy minimizing.

Carlos Simmerling

Full Professor of Chemistry at the State University of New York at Stony Brook.

Albert Einstein as a professor

He is a member of the AMBER development team.

OPLS

Developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.

A force field is used to minimize the bond stretching energy of this ethane molecule.

The functional form of the OPLS force field is very similar to that of AMBER:

Macromolecular docking

Computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules.

The quaternary structure of this protein complex would be described as a homo-trimer because it is composed of three identical smaller protein subunits (or monomers).

Free energies, estimated using parameters from molecular mechanics force fields such as CHARMM or AMBER.

Accessible surface area

Surface area of a biomolecule that is accessible to a solvent.

Illustration of the solvent accessible surface in comparison to the van der Waals surface. The van der Waals surface as given by the atomic radii is shown in red. The accessible surface is drawn with dashed lines and is created by tracing the center of the probe sphere (in blue) as it rolls along the van der Waals surface. Note that the probe radius depicted here is of smaller scale than the typical 1.4Å.

The LCPO method is also used when calculating implicit solvent effects in the molecular dynamics software package AMBER.

Sirius visualization software

Molecular modelling and analysis system developed at San Diego Supercomputer Center.

Modeling of ionic liquid

It can read output files from AMBER and CHARMM simulations, including compressed and AMBER out files.

Free energy perturbation

Method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations.

Various examples of physical phenomena

AMBER

Water model

Used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent.

A water model is defined by its geometry, together with other parameters such as the atomic charges and Lennard-Jones parameters.
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Flexible SPC water model

The OPC model is implemented within the AMBER force field.