Tutorial on running Molecular Dynamics for GIST grid generation with scripts

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Tutorial written by Trent Balius (Jan. 9, 2017).

Here are more GIST related tutorials: DOCK_3.7_with_GIST_tutorials


This is foremost for training Shoichet lab members. But we hope that the community finds this useful.

To use this tutorial you will need the following:

  • AMBER12 or higher. Here I used AMBER14.
  • GPUs to run AMBER on. In our case we uses an SGE queuing system to manage these jobs.
  • It is helpful if you have DOCK3.7 the latest version.


Grid inhomogeneous Solvation Theory (GIST) is a method for calculating thermodynamic properties of water on GIST lattice.

Here, we will use these grids for DOCKing (although, there are many other uses).

Set up environment

you can add the following to your environment file (.cshrc) for just issue them on the command line.

source python with bio_python package.

source /nfs/soft/python/envs/complete/latest/env.csh


setenv DOCKBASE "/nfs/home/tbalius/zzz.github/DOCK"


 setenv AMBERHOME /nfs/soft/amber/amber14

Put msms in your path

set path = ( /nfs/home/tbalius/zzz.programs/msms $path )

Set up directories

Prepare for AMBER

Run GIST post processing