Here are some links to a few good Amber Tutorials on setting up simulations with AmberTools. From Ross Walker (Amber developer): http://ambermd.org/tutorials/ I recommend looking at both B1 (for simple MD set up) and B4 (for simulating a compound parametrized with GAFF). From the Rizzo lab, a good s...

Hello, Because you are working with a non-protein residue, here you need to parametrize your molecule using antechamber and GAFF, which should be pretty simple for a hexane molecule. The tutorial here gives a step-by-step of the files you need to generate and load into Leap: http://ambermd.org/tutor...