Raise a warning when the atom selection breaks covalent bonds

I am running some tests on my system and I am getting quite high energies as for free energy of binding (~200 kcal/mol). In my current setup I am using resid x to y to select the ligand. Even though I have double checked the residue numbers, I still suspect that this high energy might be due to the wrong selection of atoms. Is there a way to visually inspect what happens during the simulation? Or any idea what might be causing this problem? Thanks.

[aghanbar]

Mind if I change the title of the issue to this?

Sure. I’d be happy if it could help other people.

[andrrizzi]

gave a warning about breaking any co-valent bonds during the simulation due to the wrong selection atoms

This is a great idea. Mind if I change the title of the issue to this? And thanks for sharing the combine {ligand receptor} trick. It’ll be helpful when we’ll extend the automatic pipeline to protein ligands too.