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Tinker specifications

Information


Unique identifier OMICS_25836
Name Tinker
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 8.2.1
Stability Stable
Source code URL https://dasher.wustl.edu/tinker/distribution/source/
Maintained Yes

Subtool


  • AMOEBA

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Pengyu Ren
  • person_outline Jay Ponder

Publications for Tinker

Tinker citations

 (45)
library_books

Efficient minimization of multipole electrostatic potentials in torsion space

2018
PLoS One
PMCID: 5895050
PMID: 29641557
DOI: 10.1371/journal.pone.0195578

[…] he bulk dielectric influence of water as well as from the cost of cavity formation estimated from the molecular solvent accessible surface area (SASA). The Ponder lab has reported an extension to the Amoeba force field called the generalized Kirkwood method that includes the effects of solvent as a bulk dielectric upon multipole electrostatics []. The relevant modifications to energy and gradient […]

library_books

Entropy and Polarity Control the Partition and Transportation of Drug like Molecules in Biological Membrane

2017
Sci Rep
PMCID: 5735159
PMID: 29255188
DOI: 10.1038/s41598-017-18012-7

[…] nment is not unusual, and the binding affinity between drug and membrane protein was found to be lipid-component dependent. Great efforts have been made to develop polarizable models, such as Drude,, AMOEBA–, X-POL, etc, especially those relevant to lipid bilayers,.In the present work, we used computer simulations to study the behavior of 2-APB in fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-p […]

library_books

An engineered opsin monomer scrambles phospholipids

2017
Sci Rep
PMCID: 5711885
PMID: 29196630
DOI: 10.1038/s41598-017-16842-z

[…] e for GPCRs) was modeled using the homology modeling module of modeller software and the final model was chosen based on the best DOPE score,. The model for the QUAD mutant was energy minimized using TINKER molecular modeling software (http://dasher.wustl.edu/tinker/) and the OPLSAA force field, before being used in molecular dynamics simulations (see below). RMSD of the QUAD model with respect to […]

library_books

Data driven inference for the repulsive exponent of the Lennard Jones potential in molecular dynamics simulations

2017
Sci Rep
PMCID: 5707428
PMID: 29185461
DOI: 10.1038/s41598-017-16314-4

[…] phasize however that ab-initio derived forcefields including multi-body terms have also suffered from non perfect transferability of their parameters between gaseous and condensed phase environments. AMOEBA, has been an example of a hybrid force-field that includes additional physics, and it was also calibrated using both quantum and experimental data. In the limit of a perfect model, perfect tran […]

library_books

Tinker HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04531j

2017
PMCID: 5909332
PMID: 29732110
DOI: 10.1039/c7sc04531j

[…] ative/fixed cost approach is also available: the Truncated Conjugate Gradient (TCG). TCG is implemented at the TCG1 and TCG2 levels with various refinements., The TCG approaches are a strong asset of Tinker-HP as they accurately reproduce energy surfaces at a reduced computational cost and provide analytical forces. Such an approach avoids numerical drifts appearing with iterative methods and ther […]

library_books

Level of Theory and Solvent Effects on DASA Absorption Properties Prediction: Comparing TD DFT, CASPT2 and NEVPT2

2017
PMCID: 5615680
PMID: 28869516
DOI: 10.3390/ma10091025

[…] ssian09 (Gaussian Inc., Wallingford, CT, USA) [] except for the TPA calculation, which was conducted with Dalton2016 (University of Oslo, Oslo, Norway) []. For B3LYP/AMBER optimizations, a Gaussian09/Tinker (Washington University, Saint Louis, Missouri, USA) [] protocol was applied, based on electrostatic embedding. CASPT2 and NEVPT2 computations were performed with the Molcas8 (Lund University, L […]

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