Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST
| Autor: | Crystal N. Nguyen, Ross C. Walker, Tom Kurtzman, Michael K. Gilson, Romelia Salomon-Ferrer, Steven Ramsey |
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| Rok vydání: | 2016 |
| Předmět: |
Surface Properties
Implicit solvation Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Article Set (abstract data type) Molecular dynamics Computational chemistry 0103 physical sciences Statistical physics Structure (mathematical logic) 010304 chemical physics Chemistry Solvation Proteins Water General Chemistry Grid 0104 chemical sciences Characterization (materials science) Computational Mathematics Solvation shell Solubility Thermodynamics Algorithms |
| Zdroj: | Journal of Computational Chemistry. 37:2029-2037 |
| ISSN: | 0192-8651 |
| Popis: | The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc. |
| Databáze: | OpenAIRE |
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