The directories are organized as:
HNE directory:
molX: MSLD prep, varibales.inp, analysis directory and nbond.str files for compound X
compound paramter files are inside the prep directory
msld_files: CHARMM input scripts for flattening and production
bash scripts for running MSLD flattening and production
toppar: CHARMM36m force field files
lmnmt:
molX: compounds 1-3 follow the same structure below.
charmm-cgenff:
msld: MSLD prep directory, varibales.inp file, analysis directory and nbond.str files for compound X
osp : prep directory, CHARMM and bash run scripts, python analysis file
simulation: protein, ligand psf, crd and force field stream files
opls:
msld: MSLD prep directory, varibales.inp file, analysis directory and nbond.str files for compound X
osp : prep directory, CHARMM and bash run scripts, python analysis file
simulation: protein, ligand psf, crd and force field stream files
msld_files: CHARMM input scripts for flattening and production
bash scripts for running MSLD flattening and production
multiple_distance_restraints: python script to generate protein-ligand multiple distance restraints
simularion_files: CHARMM scripts for running small MD simulation for a protein-ligand complex in a cubic water box.