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. 2018 Oct 9;14(10):5273-5289.
doi: 10.1021/acs.jctc.8b00529. Epub 2018 Sep 19.

Tinker 8: Software Tools for Molecular Design

Joshua A Rackers  1 , Zhi Wang  2 , Chao Lu  2 , Marie L Laury  2 , Louis Lagardère  3 , Michael J Schnieders  4 , Jean-Philip Piquemal  3 , Pengyu Ren  5 , Jay W Ponder  1   2
Affiliations

Tinker 8: Software Tools for Molecular Design

Joshua A Rackers et al. J Chem Theory Comput. .

Abstract

The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.

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Figures

Figure 1.
Figure 1.
Diagram showing the main component programs of the Tinker 8 package, organized into eight functional classes.
Figure 2.
Figure 2.
A schematic procedure illustrating how to construct a new Tinker program.
Figure 3.
Figure 3.
Binding free energy calculation for the model system cucurbit[7]uril and 3-amino-1-adamantanol. (A) Structures of host and guest, (B) Predicted binding pose from dynamic, (C) Experimental and predicted binding free energy.
Figure 4.
Figure 4.
Structural optimization of Deca-Alanine in the gas phase using (A) the scan program and (B) the monte program.
Figure 5.
Figure 5.
A typical thermodynamic cycle for the calculation of absolute binding free energy of host and ligand in Tinker. The completely solvated ligand and a solvent box are associated through intermediate states with gradual changes in the order parameters of vdW and electrostatics. While the order parameter of electrostatics affects both intermolecular and intramolecular interactions, the decreasing order parameter of vdW only decouples the ligand from the environment and does not change the intramolecular vdW interaction. A restraint is added to prevent the possible bad contacts and to help sampling.
Figure 6.
Figure 6.
Force Field Explorer (FFE) displaying the Dickerson dodecamer structure of B-form DNA. The expandable tree structure in the left panel provides access to coordinate and type information at the molecule, residue and atom levels.
See this image and copyright information in PMC

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References

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