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Recent Releases of openff-forcefields

openff-forcefields - Sage 2.2.1

This release adds openff-2.2.1.offxml and openff_unconstrained-2.2.1.offxml, Sage 2.2.1, which is identical to the Sage 2.2.1 release candidate. Compared to Sage 2.2.0, it fixes some linear angles to stay at 180 degrees. Code, environments, and data used to fit this force field can be found here.

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, atomic Xe, and the monoatomic ions Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I-. The parameters have been co-optimized to TIP3P water, therefore this force field also contains parameters for TIP3P, including bond length constraints.

- Python
Published by mattwthompson almost 2 years ago

openff-forcefields - Sage 2.2.1 Release Candidate 1

The new force field files in this release are from 2.2.1-rc1 tag of the Sage-2.2.1 repo.

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, and the monoatomic ions Li+, Na+, K+, Rb+, F-, Cl-, Br-, and I-. The parameters have been co-optimized to TIP3P water, therefore this contains parameters for TIP3P, including bond length constraints.

- Python
Published by j-wags almost 2 years ago

openff-forcefields - Sage 2.2.0

This release adds openff-2.2.0.offxml and openff_unconstrained-2.2.0.offxml, Sage 2.2.0, which is identical to the Sage 2.2.0 release candidate. Compared to Sage 2.1.0, it modifies some small ring internal angles and remedies issues with sulfamide geometries. Code, environments, and data used to fit this force field can be found here. Attached to that release is the release tarball, Source code, which is a static snapshot of all the code and data used to fit and benchmark the force field. The fitting process should be reproducible from this snapshot. The openff-2.2.0.offxml force field released here is identical to the file in that repo.

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, atomic Xe, and the monoatomic ions Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I-. The parameters have been co-optimized to TIP3P water, therefore this force field also contains parameters for TIP3P, including bond length constraints.

- Python
Published by amcisaac about 2 years ago

openff-forcefields - Sage 2.2.0 Release Candidate 1

This release adds openff-2.2.0-rc1.offxml and openff_unconstrained-2.2.0-rc1.offxml, Sage 2.2.0 Release Candidate 1, which modifies some small ring internal angles and remedies issues with sulfamide geometries. Code, environments, and data used to fit this force field can be found here.

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, atomic Xe, and the monoatomic ions Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I-. The parameters have been co-optimized to TIP3P water, therefore this force field also contains parameters for TIP3P, including bond length constraints.

- Python
Published by mattwthompson over 2 years ago

openff-forcefields - Sage 2.1.1

This release adds openff-2.1.1.offxml and openff_unconstrained-2.1.1.offxml, Sage 2.1.1, which has identical parameters to Sage 2.1.0 (originally released in version 2023.05.1 of the openff-forcefields package) but adds Xe van der Waals parameters from Tang, K.T., Toennies, J.P. New combining rules for well parameters and shapes of the van der Waals potential of mixed rare gas systems. Z Phys D - Atoms, Molecules and Clusters 1, 91–101 (1986).

The new OFFXML files in this release were created by running scripts/add_xe_vdw.py, available in the source tarball.

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, and the monoatomic species Xe, Li+, Na+, K+, Rb+, F-, Cl-, Br-, and I-. The non-monoatomic parameters have been co-optimized to TIP3P water, therefore this contains parameters for TIP3P, including bond length constraints.

- Python
Published by j-wags over 2 years ago

openff-forcefields - Adding more water models

This release adds the TIP4P-EW, TIP5P, and SPC/E water models. There are also some minor code changes to ensure compatibility with Python 3.12

What's Changed

  • Bump codecov/codecov-action from 3 to 4 by @dependabot in https://github.com/openforcefield/openff-forcefields/pull/81
  • Bump actions/checkout from 3 to 4 by @dependabot in https://github.com/openforcefield/openff-forcefields/pull/80
  • Revert "Bump codecov/codecov-action from 3 to 4" by @j-wags in https://github.com/openforcefield/openff-forcefields/pull/82
  • Remove use of pkg_resources by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/78
  • Test virtual site weights in water models by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/87
  • Add TIP4P-EW by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/76
  • Add SPC/E by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/75
  • Add TIP5P by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/85
  • Update versioneer setup by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/91
  • Remove more uses of pkg_resources by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/90
  • Update virtual site-related tests by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/92
  • Update setup.py by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/88
  • Uniformly lint by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/89
  • Do not yet enforce EOF consistency by @mattwthompson in https://github.com/openforcefield/openff-forcefields/pull/93

Full Changelog: https://github.com/openforcefield/openff-forcefields/compare/2023.08.0...2023.11.0

- Python
Published by mattwthompson over 2 years ago

openff-forcefields - Updating water models with vdW 0.4

This release updates water models to use version 0.4 of the vdW section of the SMIRNOFF specification.

- Python
Published by mattwthompson almost 3 years ago

openff-forcefields - Adding and updating water models

This release adds opc-1.0.1.offxml, standardizing the use of the string "kilocaloriepermole". It also adds tip3p-fb-1.1.0.offxml, which fixes a unit error in the geometric constraints and adds additional ion parameters. Finally, it adds opc3-1.0.0.offxml and tip4p_fb-1.0.0.offxml.

See docs/water-models.md for more information, and the scripts/ directory for the code to regenerate the force field files.

- Python
Published by j-wags about 3 years ago

openff-forcefields - Sage 2.1.0

The new force field files in this release contain identical physical parameters to those in openff-2.1.0-rc.1. For the fitting tarball, see the Assets section of the 2023.04.1 release.

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, and the monoatomic ions Li+, Na+, K+, Rb+, F-, Cl-, Br-, and I-. The parameters have been co-optimized to TIP3P water, therefore this contains parameters for TIP3P, including bond length constraints.

- Python
Published by j-wags about 3 years ago

openff-forcefields - OPC water model 1.0.0

This release adds our initial attempt at porting the OPC water models with associated ion parameters. See docs/water-models.md for more information, and the scripts/ directory for the code to regenerate the force field files.

- Python
Published by j-wags about 3 years ago

openff-forcefields - Sage 2.1.0 Release Candidate 1

The new force field files in this release are adapted from fb-fit/result/optimize/force-field.offxml in release_2.1.0-rc.1.tar.gz from the Assets of this release. This tarball is a modified state of https://github.com/openforcefield/sage-2.1.0 at the time this was fit.

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, and the monoatomic ions Li+, Na+, K+, Rb+, F-, Cl-, Br-, and I-. The parameters have been co-optimized to TIP3P water, therefore this force field also contains parameters for TIP3P, including bond length constraints.

- Python
Published by j-wags about 3 years ago

openff-forcefields - Version 2023.02.1 Initial Water Model Ports

This release adds our initial attempt at porting TIP3P and TIP3P-FB water models with Juong-Cheatham ion parameters. See docs/water-models.md for more information, and thescripts/ directory for the code to regenerate the force field files.

- Python
Published by j-wags over 3 years ago

openff-forcefields - Version 2.0.0 "Sage"

This force field is identical to 2.0.0-rc.2 Sage except that: * The parameter IDs have been renumbered to be sequential in all sections (for example, t70d is now t79). For more information see https://github.com/openforcefield/openff-sage/pull/1 and the attached old-id-to-new-id-map.json file. * The openff_unconstrained-2.0.0.offxml file has had TIP3P geometry constraints added, but all other hydrogen bonds remain unconstrained. * Formatting cleanup and cosmetic changes

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, and the monoatomic ions Li+, Na+, K+, Rb+, F-, Cl-, Br-, and I-. The nonbonded parameters in this force field were optimized assuming use with TIP3P water, and so TIP3P parameters are included in the force field.

- Python
Published by j-wags almost 5 years ago

openff-forcefields - Version 2.0.0-rc.2 "Sage" Release Candidate

This major release candidate is identical to v2.0.0-rc.1 Sage except that the angle value for a16 has been changed to 180.0 * degree, as the previous value of 183 * degree causes geometry optimizers to fail to converge.

This force field is applicable to druglike molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, and the monoatomic ions Li+, Na+, K+, Rb+, F-, Cl-, Br-, and I-. The nonbonded parameters in this force field were optimized assuming use with TIP3P water, and so TIP3P parameters are included in the force field.

Provided that early use of this force field shows no major deficiencies, this may be promoted to the full Sage release.

- Python
Published by j-wags almost 5 years ago

openff-forcefields - Version 2.0.0-rc.1 "Sage" Release Candidate

The contents of this major release candidate are adapted from https://github.com/openforcefield/openff-sage/releases/tag/2.0.0-rc.1. See that release's notes and assets for more details.

Provided that early use of this force field shows no major deficiencies, this may be promoted to the full Sage release.

- Python
Published by j-wags almost 5 years ago

openff-forcefields - Version 1.3.1 "Parsley" Update

This bugfix release is identical to 1.3.1-alpha.1. Please see those release notes (https://github.com/openforcefield/openff-forcefields/releases/tag/1.3.1-alpha.1) for details.

- Python
Published by j-wags almost 5 years ago

openff-forcefields - Version 1.3.1-alpha.1 "Parsley" Update candidate

Short summary

The new force field files in this release are adapted from the openff-1.3.0 release, except that two angle parameters have been reverted to their original values from smirnoff99Frosst 1.1.0.

Full Summary

The ability of the Parsley line of force fields ability to reproduce the tetrahedral geometry of certain sulphonamides (especially primary sulphonamides) has progressively and subtly degraded between releases, cumulating in OpenFF 1.3.0 yielding a O-S-N valence angle of < 90 deg for certain molecules while angle of ~109.5 would be more expected.

Simulating CC1=CC=C(C=C1)S(=O)(=O)N in vacuum using OpenFF 1.3.0, for example, shows an average O-S-N valence angle of 76.26 (+/- 0.21)

This issue has been tracked to the a30 ([*:1]~[#16X4:2]~[*:3]) and a31 ([*:1]-[#16X4,#16X3+0:2]-[*:3]) valence angle parameters, whereby the equilibrium angle has monotonically reduced while simultaneously the force constant has increased:

```

| | SMIRNOFF99Frosst | Parsley 1.2.0 | Parsley 1.3.0 | | |------------------|----------------|----------------| | | k | theta | k | theta | k | theta | |-----|-------|----------|-------|--------|----------------| | a30 | 140.0 | 109.5 | 201.1 | 104.2 | 220.7 | 99.1 | | a31 | 120.0 | 109.5 | 152.3 | 96.3 | 188.4 | 89.8 |

(k in kcal / mol, theta in deg) ``` This has seemingly in turn resulted in the degradation of protein-ligand binding free energies for certain molecules which contain sulphonamide moieties (primarily primary sulphonamide groups). This potentially also affects related hypervalent substituents (e.g. hypervalent nitrogens) although currently only issues with sulphonamides has been observed.

We believe this issue arose due to the valence angle being trained to both sulphur containing rings in addition to molecules where the sulphur would be expected to be tetrahedral, whereby ring containing sulphur molecules would likely drive the angles to be smaller than 109.5 degrees. We are now actively working to validate this hypothesis and come up with a sustainable resolution for future releases.

For now given the potential severity of the issue, it has been decided that we will make an alpha patch release of OpenFF 1.3.0, numbered OpenFF 1.3.1-alpha.1, which has the values of a30 and a31 reset to their smirnoff99Frosst 1.1.0 values.

Provided that benchmarks show this issue as resolved OpenFF 1.3.1-alpha.1 will become a full release -> OpenFF 1.3.1.

- Python
Published by j-wags about 5 years ago

openff-forcefields - Version 1.3.0 "Parsley" Update

The new force field files in this release are adapted from result.offxml in release_1.3.0.tar.gz from the Assets of Version 1.3.0 "Parsley". See that release page for more details.

- Python
Published by j-wags over 5 years ago

openff-forcefields - Version 1.2.1 "Parsley" Update

This bugfix release manually changes two bond force constants (b24 and b27) to resolve an issue seen in propyne substituents when using hydrogen mass repartitioning with a 4fs timestep. Full details are available at https://github.com/openforcefield/openforcefields/issues/19 and in the reproduce_propyne_hmr.ipynb notebook in the release assets on GitHub.

- Python
Published by j-wags almost 6 years ago

openff-forcefields - Version 1.2.0 "Parsley" Update

The new force field files in this release are adapted from result.offxml in release_1.2.0.tar.gz from the Assets of Version 1.2.0 "Parsley" Update. See that release page for more details.

- Python
Published by j-wags about 6 years ago

openff-forcefields - Version 1.1.1 "Parsley"

This bugfix release contains following changes: (1) Addition of monatomic ion LibraryCharges.

- Python
Published by dotsdl about 6 years ago

openff-forcefields - Version 1.0.1 "Parsley"

This bugfix release contains following changes: (1) Addition of monatomic ion LibraryCharges.

- Python
Published by dotsdl about 6 years ago

openff-forcefields - Version 1.1.0 "Parsley" Update

The new force field files in this release are adapted from result.offxml in the Assets of Version 1.1.0 "Parsley". A detailed description of the updates in this version are available at that link.

- Python
Published by j-wags over 6 years ago

openff-forcefields - Version 1.0.0 "Parsley"

The new force field files in this release are adapted from result.offxml in release_1.0.0_RC2.tar.gz from the Assets of OpenFF "parsley" 1.0.0-RC2: Fitting Valence with QM Data

A blog post summarizing the benchmarking of this FF will be published in the near future at https://openforcefield.org/news/

- Python
Published by j-wags over 6 years ago

openff-forcefields - OpenFF-1.0.0 Release Candidate 2

Adds OpenFF-1.0.0 Release Candidate 2. This is taken from the QM-only refit performed in https://github.com/lpwgroup/forcebalance-qcarchive/releases/tag/v0.0.9. The new files, openff-1.0.0-RC2.offxml and openff_unconstrained-1.0.0-RC2.offxml, are copies of result.offxml in that release tarball, with tabs converted to spaces, author and date fields filled, and cosmetic attributes removed. The constraints in openff-1.0.0-RC2.offxml are copied from release candidate 1.

- Python
Published by j-wags over 6 years ago