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English
On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes.
scientific article published on August 2010
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Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
title
On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes
(English)
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
main subject
AMBER
0 references
force field
0 references
author
Michal H Kolář
series ordinal
1
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
Karel Berka
series ordinal
2
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
Pavel Hobza
series ordinal
4
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
author name string
Petr Jurecka
series ordinal
3
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
publication date
1 August 2010
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
published in
ChemPhysChem
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
volume
11
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
issue
11
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
page(s)
2399-2408
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
cites work
Double-Helical → Ladder Structural Transition in the B-DNA is Induced by a Loss of Dispersion Energy
1 reference
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Ab initio molecular dynamics: Propagating the density matrix with gaussian orbitals. IV. Formal analysis of the deviations from born-oppenheimer dynamics
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7 January 2021
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Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
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7 January 2021
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Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock
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Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
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7 January 2021
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Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples
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The interaction of carbohydrates and amino acids with aromatic systems studied by density functional and semi-empirical molecular orbital calculations with dispersion corrections
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7 January 2021
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Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions
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7 January 2021
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Further analysis and comparative study of intermolecular interactions using dimers from the S22 database
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7 January 2021
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True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine...cytosine, adenine...thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison w
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7 January 2021
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Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein.
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7 January 2021
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Accurate description of van der Waals complexes by density functional theory including empirical corrections
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7 January 2021
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Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared withab initioquantum mechanics calculations
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reference URL
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7 January 2021
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Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes
1 reference
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7 January 2021
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Development and testing of a general amber force field
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7 January 2021
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A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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7 January 2021
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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
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7 January 2021
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Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes
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7 January 2021
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Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-functional calculations
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7 January 2021
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Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: a new efficient method to study intermolecular interaction energies
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7 January 2021
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Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry
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7 January 2021
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Interaction energy contributions of H-bonded and stacked structures of the AT and GC DNA base pairs from the combined density functional theory and intermolecular perturbation theory approach
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7 January 2021
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Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures
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Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen
1 reference
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Automatic atom type and bond type perception in molecular mechanical calculations
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Comparison of simple potential functions for simulating liquid water
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7 January 2021
based on heuristic
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Identifiers
DOI
10.1002/CPHC.201000109
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
PubMed publication ID
20629063
1 reference
stated in
Europe PubMed Central
PubMed publication ID
20629063
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20629063%20AND%20SRC:MED&resulttype=core&format=json
retrieved
7 February 2020
ResearchGate publication ID
45186301
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