AMBER pipeline

AMBER specifications


Unique identifier OMICS_13306
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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  • person_outline D.A. Case <>
  • person_outline Ross Walker <>

Publications for Assisted Model Building with Energy Refinement

AMBER IN pipelines

PMCID: 5627182
PMID: 28978442
DOI: 10.1016/j.bpj.2017.08.010

[…] 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 […]

PMCID: 5737849
PMID: 28505313
DOI: 10.1093/nar/gkx418

[…] 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). […]

PMCID: 4735121
PMID: 26829126
DOI: 10.1371/journal.pone.0147761

[…] and temperature was control with langevin thermostat (1 atm, 300k) [44]. long-range electrostatic interactions were computed by employing particle mesh ewald (pme) with the default setting in amber14 [45, 46]. the cutoff distances for the long range electrostatic and van der waals interactions were set to 10.0 å. the shake algorithm was used for the covalent bonds involving hydrogen [47]. […]

PMCID: 4846865
PMID: 27118724
DOI: 10.1038/srep25070

[…] 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 […]

PMCID: 5125647
PMID: 27893774
DOI: 10.1371/journal.pone.0166935

[…] coupling constants for temperature and pressure were 5.0 and 2.0 ps, respectively, no restraints on the protein. the md simulation trajectories were analyzed with vmd [32] and the ptraj module of amber. the resulting final frame structures were first minimized with amber (similarly to the last step of the initial minimization) and then visually examined with pymol (schrödinger, inc.)., […]

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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