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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

Subtools


  • AmberTools
  • MM-PBSA

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Documentation


Maintainers


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

Publications for Assisted Model Building with Energy Refinement

AMBER citations

 (415)
library_books

High resolution AFM structure of DNA G wires in aqueous solution

2018
PMCID: 5958085
PMID: 29773796
DOI: 10.1038/s41467-018-04016-y

[…] exposed g-tetrads., the long g-wire models were simulated using md approaches for relaxation in explicit solvent. the input files were prepared using xleap (ambertools15) and simulated using amber 10 with the ff99 dna force field. models underwent unrestrained energy minimization of 1000 steps of steepest decent followed by 9000 steps of conjugant gradient method to remove clashes […]

library_books

Defining a conformational ensemble that directs activation of PPARγ

2018
PMCID: 5935666
PMID: 29728618
DOI: 10.1038/s41467-018-04176-x

[…] to the h++ server (http://biophysics.cs.vt.edu/h++) to determine the state of titratable protons at ph 7.4, along with more realistic rotamers for some residues. this h++ pdb file was then given amber names for the various protonation states of histidine determined by h++ using pdb4amber (ambertools14). pdb files of cysteine-btfa residue was created through modification of a cysteine residue […]

library_books

Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches

2018
PMCID: 5929558
PMID: 29715318
DOI: 10.1371/journal.pone.0196484

[…] current study, a cluster is a group of sequences sharing a minimum of 80% of the sequence identity is known to be a cluster., md simulations of all the selected complexes were carried out by using amber 14 molecular dynamics package []. to neutralize the systems counter na+ ions and hydrogens were added. the tleap package of amber was utilized to perform this process. a tip3p water box of 8.0 […]

library_books

Substrate bound outward open structure of a Na+ coupled sialic acid symporter reveals a new Na+ site

2018
PMCID: 5931594
PMID: 29717135
DOI: 10.1038/s41467-018-04045-7

[…] system was then solvated in a rectangular box (90 × 90 × 106 å3) containing 150 mm na+ and cl− resulting in final system sizes of ~86,000 atoms. all system files were then converted from charmm to amber format with in house scripts. simulations were carried out using the ff14sb amber parameter set for the protein, glycam06 for the neu5ac, the joung-chetham parameters for the monovalent ions […]

library_books

On the contributing role of the transmembrane domain for subunit specific sensitivity of integrin activation

2018
PMCID: 5893634
PMID: 29636500
DOI: 10.1038/s41598-018-23778-5

[…] of 17 å for the water layer above and below the protein. the total system size is ~60,000 atoms, including tip3p water molecules and cl- counter ions., all md simulations were performed using the amber 14 suite of programs, the ff99sb force field for the proteins, the lipid14 force field for the lipids, and the tip3p water model. the particle mesh ewald method was used to treat long-range […]

library_books

A quantum mechanical computational method for modeling electrostatic and solvation effects of protein

2018
PMCID: 5882933
PMID: 29615707
DOI: 10.1038/s41598-018-23783-8

[…] systems (pdb id: 1bhi and 2kcf) using hf and dft (m06-2×) methods with 6-31 g* basis set. the geometries of the two proteins were optimized with amber99sb force field using sander module of the amber program in order to remove bad contacts prior to subsequent ab initio calculations. the calculated electrostatic potential using the ee-gmfcc-chg were compared to that of the fs qm […]


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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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