This repo contains the scripts to simulate the carbonic anhydrase II enzyme with Orb.

3ks3-withHCO2.py is the main python script it uses 3ks3-withHCO2noGOL.xyz as a starting file and frozenatoms.dat contains the indices of the atoms to freeze in the simulation.

There are five trajectory files demonstrating the proton hopping to His64 event (3ks3-withHnoGOLwCO2HHop.xyz), the proton hopping event onto Glu106 (3ks3-withHnoGOLwCO2HHopGlu106.xyz)  and the bicarbonate reaction event. (reaction_traj_27920.0fs_H4474-O4802_BB__O4802-C5499_BF) The bicarbonate reaction trajectory was captured with the the automatic reaction detection script. (3ks3-withHCO2noGOL-reactcapture.py)
The timestep for these trajectories is 10 fs. 

Two longer trajectories are also included with a 5 ps timestep: 3ks3-withHnoGOLwCO2topocket.xyz shows the migration of CO2 into the hydrophobic binding site 3ks3-withHnoGOLwCO2HCO3.xyz shows the bicarbonate ion stably bound to the zinc.


Barrier.py and clean-rdf-plot.py are scripts to generate the plots in the paper, using the .dat files.

3ks3-withHnoGOLwCO2.pdb is a pdb file that matches the xyz trajectory files.