MD simulation for a protein with Cu ions in the structure

User discussions
1

GROMACS version:2022.2
GROMACS modification: No

Hi everyone, I am currently working with a protein which has 6 Cu ions coordinated in its structure, I would like to know how I need to correctly run the simulation because it’s my first time running a MDS considering ions too. Among the solution I red there is the possibility to use harmonic restraint to restrain the Cu ions to the residues to which they are coordinated using [bonds] type 6 in the topology file. To apply this type of restraint I saw that for a correct syntax I need to specify the values of distance b0(nm) and the force [ kJ(mol)-1(nm)-2 ], I was wondering how to choose these 2 values. For the distance can I measure from the pdb the distance between the Cu and the atoms to which are coordinated and consider those values? While for the force how can I decide which value I need to use?

Thank you

2

Hi,
I have used a similar approach for Zn coordinated to a proteins. For b0 I have used the distance from the pdb file (or average distance, in case of same type of coordinating residue)
for k0 I used 4000 kJ/(mol nm^2). This was working in my case.
You can check if simular setting keeps the ion in the coordination position in your case, otherwise you can tune a little kb value.
\Alessandra