SSTMap Solvation Structure and Thermodynamic Mapping

SSTMap Github Repository

The latest version of SSTMap can be found at our Github or can be installed with Anaconda’s conda package manager. For more information please see our previous post regarding installation of SSTMap.

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SSTMap Update - Release of version 1.1.0

We are pleased to anounce the release of SSTMap v1.1. This new version is base on python 3 with backward compatability with python 2.7. Now the version of python is not an issue but we recomnd the use of python 3 since future development will target this version of python.

In addition to adding support for python 3, SSTMap v1.1.0 incomporate some code optimizations and the ability to handle peridic boundary condition on non-orthorombic boxes.

As with previous releases we recoment to use conda for installation. If this is your first time installing SSTMap then use the following command to install the lates version of SSTmap: conda install sstmap -c omnia -c solvationtools.
If you already had SSTmap installed then use the following command to update to the latest version: conda update sstmap.

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JCTC Paper Published

Our paper titled “Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories” has been published in the Journal of Chemical Theory and Computation: DOI: 10.1021/acs.jctc.7b00592.

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Installing SSTMap

The main requirement for installation of SSTMap is the anaconda python distribution. If you are not familiar with Anaconda, please have a look at SSTMap is implemented in python 2.7, so if you do not have the anaconda installation, downlaod the anaconda for python 2.7, as shown below. Alternatively, if you have a an anaconda installation for python 3.6, you can create a python 2.7 enviornment to run sstmap.

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Running SSTMap Calculations

SSTMap implements two approaches for mapping water structure and thermodynamics on to solute surfaces, such as protein binding sites, the hydration site analysis (HSA) and Grid Inhomogeneous Solvation Theory (GIST). The command lines to run each of these analyses are simply run_hsa and run_gist which are the main command-line tools in SSTMap. Here we provide examples of the command line arguments required to run these analyses with different popular MD packages.

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