AmberTools 19 – Molecular Dynamics Simulation

AmberTools 19

:: DESCRIPTION

AmberTools consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models.

AmberTools consists of 7 main codes
NAB build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models
antechamber Create force fields for general organic molecules
ptraj Analyze trajectories from Amber or CHARMM
tleap and xleap Basic preparation program for Amber simulations
sleap replaces and expands tleap
sqm semiempirical and DFTB quantum chemistry program
pbsa Performs numerical solutions to Poisson-Boltzmann models

::DEVELOPER

AMBER Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window with Cygwin

:: DOWNLOAD

AmberTools

:: MORE INFORMATION

Citation

D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods.
The Amber biomolecular simulation programs.
J. Computat. Chem. 26, 1668-1688 (2005).

Forcefield_PTM – AMBER Forcefield Parameters for Post-translational Modifications

Forcefield_PTM

:: DESCRIPTION

Forcefield_PTM is a set of self-consistent AMBER forcefield parameters for frequently occurring post-translational modifications (PTMs).

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications.
Khoury GA, Thompson JP, Smadbeck J, Kieslich CA, Floudas CA.
J Chem Theory Comput. 2013 Dec 10;9(12):5653-5674.

Forcefield_NCAA – AMBER Forcefield Parameters for Non-canonical Amino Acids

Forcefield_NCAA / FFNCAA

:: DESCRIPTION

Forcefield_NCAA is a set of self-consistent AMBER forcefield parameters for non-canonical amino acids. It allows you to design and derivatize peptides containing NCAAs for use as drugs.

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family.
Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA.
ACS Synth Biol. 2014 Dec 19;3(12):855-69. doi: 10.1021/sb400168u.

AMBER 15 – Assisted Model Building with Energy Refinement

AMBER 15

:: DESCRIPTION

AMBER (Assisted Model Building with Energy Refinement) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

::DEVELOPER

AMBER Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window with Cygwin
  • Fortran 95, C and C++ compilers.

:: DOWNLOAD

AMBER

:: MORE INFORMATION

Citation

D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programsJ. Computat. Chem.26, 1668-1688 (2005).

Yammp Conversion Tools – Simulation of Yammp Models in CHARMM or Amber

Yammp Conversion Tools

:: DESCRIPTION

The Yammp Conversion Tools contain a set of utilities that allow the simulation of Yammp models in CHARMM or Amber.

::DEVELOPER

NIH Research Resource Center for the Development of Multiscale Modeling Tools for Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Perl

:: DOWNLOAD

Yammp Conversion Tools

:: MORE INFORMATION

Citation:

Michael Feig, John Karanicolas, Charles L. Brooks, III: MMTSB Tool Set (2001), MMTSB NIH Research Resource, The Scripps Research Institute