Hi Peter, Thanks for your help. Is there a straightforward way to do this with exactly 10 explicit waters. Also I have never used Amber before so if you get a chance would you mind posting the code I'd need to run to set up this system in AmberTools and run it in OpenMM? I get my initial coordinates...

Also, please ignore the system.addSolvent line in the script above. When I tried to add that line the script failed.

Ok, I used antechamber to generate the prmtop and inpcrd files and MD works great with one molecule. How do I then add explicit waters? In particular I want to add exactly 10 explicit waters to the system. My python script is included down below. Since I am not using the Modeller class I do not know...

I am having some difficulty getting started with OpenMM. My goal is to be able to take any arbitrary organic molecule surrounded by explicit water molecules and to run classical molecular dynamics. I want to generate an animation of the molecular dynamics that can be viewed in jmol. Right now I cann...