openmmforcefields/charmm

CHARMM forcefield conversion tools for OpenMM

This directory contains files and scripts needed to convert the CHARMM forcefield to OpenMM ffxml files

Manifest

• 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

Dependencies

• ParmEd - for parameter/topology conversion

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.