Useful links:

Tools

Here are a number of Tools that you may find helpful when conducting research with the AMBER software suite. Clicking on each chapter heading will take you to a new page of abstracts describing each tool. If you can see what you want from the titles, you may go directly to each tool's page from here.

• 9.1 Unix and Editing Commands
  9.1.1 Getting Started with Linux
  9.1.2 Learning the Unix Command-line
  9.1.3 Ryans Linux Tutorials
  9.1.4 Vi Text Editor
  

• 9.2 Visualization Software
  9.2.1 Download VMD and Manual
  9.2.2 Using VMD with AMBER
  9.2.3 VMD Movie Making
  9.2.4 Official VMD Tutorials
  9.2.5 Download Chimera-X and Manual
  

• 9.3 Plotting
  9.3.1 XMGrace
  9.3.2 Tutorial - Line plotting and histograms
  9.3.3 Pyplot
  9.3.4 Pyplot Tutorials through MolSSI
  

• 9.4 Jupyter Notebooks and Python
  9.4.1 An Introduction to PYTRAJ
  9.4.2 Simulating Crystals with AMBER Molecular Dynamics - Jupyter notebook version
  9.4.3 Using Jupyter notebook remotely
  9.4.4 Using NGLView for protein visualization in Jupyter notebook
  9.4.5 Trajectory rendering and movie making with NGLView
  9.4.6 Real time molecular dynamics simulation and visualization
  

• 9.5 Free Energy Tools
  9.5.1 CANDO - graphical interface for building some Amber systems and TI calculations
  9.5.2 DDBoost - build TI calculations and analyze output