Dear AMBER users,
I've run an MD simulation of an enzyme containing the cuboidal [4Fe-4S] cluster in the active site and the SAM molecule that coordinates to metal cluster.
The same simulation contains O2 molecules within the water solvent. I am interested in looking at the number of O2 molecules that enter the active site and approach the metal cluster over the simulation and track the route of the identified O2 molecule(s).I looked at the possibilities to retrieve so by using cpptraj by I failed with the hbond command (because there is no h-bonding between O2 and [4Fe-4S] cluster) as well as looking at native contacts or using the closest command.
I failed with the implicit ligand sampling tool in VMD too and I want to ask you if you know of any other turnaround to calculate that.
Kind regards,
Damiano Spadoni
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Received on Mon Apr 12 2021 - 10:00:03 PDT
