ProtonHopping

Data and code for Proton Hopping project. The gaol of this project is to develop a method to calculate energies of proton hopping in hydrogen-bonded water-water and protein-water systems. See a brief project summary here

Current Status

MCCE simulation protocol under optimization. Current inputs can be reproduced as follows. All scripts should be run from scripts subfolder.

Step 1:

Generate MCCE compatible structure of gramicidin channel.

python prep_gramicidin_structure.py

Step 2:

Insert gramicidin into a membrane (using IPECE program).

python insert_membrane.py

Step 3:

Re-build full gramicidn-membrane MCCE compatible structure

python prep_mem_gramicidin_structure.py

Step 4:

Fix membrane atom names so that they conform to MCCE atom typing for membrane atoms.

python fix_mem_atom_names.py

Step 5:

Generate a rectangular gird and place water oxygen atoms, remove oxygens that are in vdw clash with the system.

python place_water_oxygens.py

Step 6:

Generate water geometries from the oxygen atoms using tleap.

tleap -f tleap_type_waters.in

Step 7:

For each oxygen atom, enumerate orientational conformers, resulting in N conformer per water, where N can be 5, 10, 15, 20, 25.

python generate_water_conformers.py