08 Dec 2017
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.
06 Jun 2017
The main requirement for installation of
SSTMap is the anaconda python distribution. If you are not familiar with Anaconda, please have a look at continuum.io/why-anaconda. 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.
03 Jun 2017
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_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.
09 May 2017
run_gist output several files, which are named after the prefix specfied under
-o flag. In this post, we will describe these outputs.