AMBER specifications

Information


Unique identifier OMICS_13306
Name AMBER
Alternative name Assisted Model Building with Energy Refinement
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++, Fortran, Python
License Commercial
Computer skills Advanced
Version 17
Stability Stable
Maintained Yes

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Maintainers


  • person_outline D.A. Case <>
  • person_outline Ross Walker <>

AMBER articles

AMBER citations

 (6)
2017
PMCID: 5627182

[…] all his residues were modeled in the uncharged state with the ε-protonated nitrogen., md runs were carried out using the gpu implementation of pmemd (52). trajectories were analyzed through cpptraj amber15 tools (53) and visualized with vmd (version 1.9.1 (54)). the identification of key interactions was aided by other visualization tools, such as moe and pymol (version 1.6 (55)). to quantify […]

2017
PMCID: 5737849

[…] the experimental nmr restraints during the first 120 ns of the simulations. the specifics of this procedure are extensively discussed elsewhere (56). all simulations were conducted using the amber 14 program suite (57)., the analyses were performed with the cpptraj program (58). vmd and pymol were used for visualization while raster3d was used to produce the molecular images (59,60). […]

2016
PMCID: 4846865

[…] use in simulation was prepared in gaussian09 utilizing the hf/631-g(d) basis set. topology and force field parameters for the structure were generated by antechamber, a set of tools included in the amber suite. the structure was then inserted into two sites on the dmf5 tcr: r27α (cdr1α) and f100β (cdr3β), each mutated to cysteine for probe conjugation. pre-production and production trajectories […]

2014
PMCID: 3985865

[…] the final set of distance and angle constraints was used to produce 500 structures in cyana, and the 100 structures with the smallest constraint violations were refined by molecular dynamics using amber 9.31 the final refinement was performed by simulated annealing and energy minimization that employed a generalized-born (gb) continuum solvent model.32 procheck was used for analysis of the jaz […]

2014
PMCID: 3985902

[…] package.27 nucleotides structures were diagrammed with chemdraw ultra 12.0 and the pmf plot was generated using matlab.61,62, the initial molecular dynamics simulations were run with the standard amber ff10 force field.25 for system 1 and system 4, the native structures shown in table 1, three independent simulations were run for 1 μs each. three independent trajectories were run for systems […]

AMBER institution(s)
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA; Departments of Medicinal Chemistry, Pharmaceutics & Pharmaceutical Chemistry, and Bioengineering, University of Utah, Salt Lake City, UT, USA; National Institute of Environmental Health Sciences, Laboratory of Structural Biology, NC, USA; Fachbereich Biologie und Informatik, J.W. Goethe-Universität, Frankfurt/Main, Germany; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA; Department of Chemistry, Pennsylvania State University, University Park, PA, USA; Department of Computer Science, Virgina Tech, Blacksburg, VA, USA; Department of Chemistry, Stony Brook University, Stony Brook, New York, NY, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
AMBER funding source(s)
This work was funded in part by the National Science Foundation through the Scientific Software Innovations Institutes program—NSF SI2-SSE (NSF1047875 & NSF1148276)—grants and also by the University of California (UC Lab 09-LR-06–117792) grant.

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