Water plays an important thermodynamic role in molecular recognition, which includes many biologically relevant processes such as hydropobic aggregation, protein-ligand binding, and the formation of lipid bilayers. 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 provides high resolution three dimensional characterizations of water structural and thermodynamic quantities by applying Inhomogeneous Fluid Solvation Theory on explicit solvent molecular dynamics trajectories to map out solvent properties. The implementation into CPPTRAJ, called GIST-cpptraj, utilizes the simple and easy to use command line interface provided by CPPTRAJ and is open sourced and freely distributed. We have also developed several open sourced tools to assist end users in performing GIST analysis. In this study we present GIST-cpptraj displaying its capabilities, ease of use, utility, and its support within the Amber MD community.

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

254th National Meeting (2017)

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