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Files

Matt Thompson d78f2b8258 Update docstrings, run in CI (#240 )

* Update docstrings, run in CI

* Do not necessarily assume ff14SB port is installed

* Remove some references to `simtk`

$ grep -r simtk . | wc -l
       0

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

2022-10-25 11:27:40 +00:00

dhfr

Encapsulate test scripts within dhfr/ directory

2018-02-13 10:46:10 -08:00

files

Update CHARMM to July 2020 release; delete toppar so parameters are retrieved before conversion

2021-02-04 20:05:26 -05:00

tests

Add missing waterbox test files

2019-11-30 11:46:24 -05:00

convert_charmm.py

Update all simtk.openmm -> openmm and simtk.unit -> openmm.unit imports for OpenMM 7.6; pin to >=7.6

2021-08-27 17:48:27 -07:00

Dockerfile

Adding first draft of direct comparison to CHARMM

2018-02-12 00:02:09 -08:00

energy.py

Update docstrings, run in CI (#240 )

2022-10-25 11:27:40 +00:00

README.md

Update CHARMM to July 2020 release; delete toppar so parameters are retrieved before conversion

2021-02-04 20:05:26 -05:00

test_charmm.py

Update docstrings, run in CI (#240 )

2022-10-25 11:27:40 +00:00

README.md

CHARMM forcefield conversion tools for OpenMM

This directory contains files and scripts needed to convert the CHARMM forcefield to OpenMM ffxml files Updated to July 2020 release from http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

Manifest

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)

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.

Converting

Retrieve and unpack the CHARMM files

wget http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul20.tgz
tar zxf toppar_c36_jul20.tgz

Convert the solvent force fields

python convert_charmm.py --verbose --in files/waters.yaml

Convert non-solvent force fields

python convert_charmm.py --verbose --in files/charmm36.yaml

CHARMM docker image

Prerequisites

Docker toolbox
CHARMM lite nonprofit/academic version (free) - downloaded as charmm.tar.gz

Building the docker image

After starting the Docker daemon, run

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

Running CHARMM

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