Tutorial on running Molecular Dynamics for GIST grid generation

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

Disclaimer

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.
  • AMBERTOOLS.
  • 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.

Introduction

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).

Prepare for AMBER

  • download 4NVE form the PDB brake it into receptor and ligand pieces.
  • download pdb 4NVA form the PDB align it to 4NVE and out put waters that are close to the ligand.
  • here is one way to do it:



Run AMBER

Run GIST post processing

Combining GIST grids

Run convergence analysis