toppar/ - CHARMM36 toppar files taken and unzipped from (http://mackerell.umaryland.edu/charmm_ff.html) Jan 2016.
ffxml/ - converted OpenMM ffxml files for CHARMM36
tests/ - test systems for CHARMM36
charmm36.yaml - yaml input file needed to drive bundling by convert_charmm.py
convert_charmm.py - script to convert CHARMM top and par files to ffxml
test_charmm.py - script to test CHARMM conversion after convert_charmm.py has been run
energy.py - validate energies against CHARMM lite academic version inside a docker container (see below)

Dependencies

Notes

Notes on files that were excluded from conversion:

There are two glycolipid stream files with duplicate dihedrals with different values. According to discussion with Alex MacKerell, the carb glycolipid file should be used so the lipid glycolipid stream file was excluded.
toppar_all36_prot_aldehydes.str and toppar_all36_na_modifications.str have different values for the angle of atom types O CD CT2. These files should not be used in the same system so both were excluded. A new atom type is needed to correct this. If needed, CGenFF can be used for aldehydes or the user can convert these files at their own risk.

After starting the Docker daemon, run

docker build -t omnia/charmm-lite:c40b1 .

The CHARMM executable is /charmm/c40b1_gnu/exec/gnu/charmm

To manually start the docker image (for testing purposes):

docker run -i -t omnia/charmm-lite:c40b1 /bin/bash

Running comparison
------------------

To run the comparison from this directory:

python energy.py dhfr