Hello everyone.

I'm currently facing the following problem: I'm doing with Amber MD simulations on a protein that has metals ions (zinc and copper) in it to perform its biological activity and to be more stable. When I do conformational clustering with Amber, I find out that in most of the representative structures (one for each cluster), the metal ions are not in the correct position, instead they were moved some angstrom away from the protein. I include some pics to make the problem more understandable: the red structure is the one representing cluster 0 while the purple one is the initial pdb structure used for the simulation. It can be seen that the copper ion is quite distant from the original position as it runned away.

Do need to apply some restrains on the ions in the simulation .in files (minimization, heating, equilibration and real med simulation) or do I need to change some parametrizations in the tleap protocol I used?

I report the latter here:

module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 cuda/12.2 amber/22.5-23.5 # Load the necessary modules for using Amber

pdb4amber -i dimer_c.pdb -o dimer_c_amber.pdb # Make the PDB file readable by Amber

reduce -Trim dimer_c_amber.pdb > dimer_c_amber_noH.pdb

tleap

source leaprc.protein.ff19SB # Load the force field for proteins

loadoff atomic_ions.lib # Load the library file for divalent ions

loadamberparams frcmod.ionslm_1264_opc # Load the parameter file for divalent ions

source leaprc.water.opc # Load the opc water model

dimer = loadpdb dimer_c_amber_noH.pdb

charge dimer

solvateOct dimer OPCBOX 10.0 # Set a truncated octahedron with a thickness of 10 Angstrom as the solvent box

addIonsrand dimer Na+ #Na Cl- #Cl # Set the number of ions to add to neutralize the system charge (see Matlab script)

saveAmberParm dimer dimer_c_amber_noH_solv.prmtop dimer_c_amber_noH_solv.inpcrd # Save the topology parameters and coordinates of the new structure

check dimer

savepdb dimer dimer_c_amber_noH_solv.pdb # Save the new structure

Thank you very much