GROMACS version:2018.1
GROMACS modification: No
I want to study the interactions that can form by the amino acid residues of an enzyme with a metal ion using simulation results. The Chimera software has the option to study the metal geometry. Does this option available only for the metal ions already in the enzyme and not for the ions we introduce to the enzyme system? Because in my case, I can study the metal geometry only for the ions that were already in the enzyme but not for the ion I added to the system as a foreign body.
How can we solve this issue and is there any other way to analyse the enzyme-metal interactions?