From 6724db4b9456dcdad3ba856d05bcd8c44765ddb6 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Mon, 8 Jul 2019 19:06:20 -0700 Subject: [PATCH 1/5] add s99F-1.0.10 from OFF repo (exptl), add const section, update README --- README.md | 6 +- .../offxml/smirnoff99Frosst-1.0.10.offxml | 339 ++++++++++++++++++ 2 files changed, 344 insertions(+), 1 deletion(-) create mode 100644 smirnoff99frosst/offxml/smirnoff99Frosst-1.0.10.offxml diff --git a/README.md b/README.md index 9035d8b..5752f34 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,7 @@ DOIs for each force field in this repository can be found in the following table | Filename | DOI | | -------- | --- | +| smirnoff99Frosst-1.0.10.offxml | No DOI yet | | smirnoff99Frosst-1.0.9.offxml | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3256444.svg)](https://doi.org/10.5281/zenodo.3256444) | | smirnoff99Frosst-1.0.8.offxml | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2565295.svg)](https://doi.org/10.5281/zenodo.2565295) | | smirnoff99Frosst-1.0.7.offxml | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1186466.svg)](https://doi.org/10.5281/zenodo.1186466) | @@ -105,11 +106,14 @@ Additionally, with ParmEd, it should be possible to convert parameterized OpenMM - [Version 1.0.7](https://dx.doi.org/10.5281/zenodo.1186466): Add hydroxyl hydrogen radii (as per SMIRNOFF initial paper); remove generics with pure wildcards (not even elemental types). - [Version 1.0.8](http://doi.org/10.5281/zenodo.2565295): Fix human error in hydroxyl hydrogens; fix bond parameters between hydrogen and divalent carbons ([issue #81](https://github.com/openforcefield/smirnoff99Frosst/issues/81)); and fixed SMIRKS patterns for angle parameters around trivalent carbon in 5-membered rings ([issue #84](https://github.com/openforcefield/smirnoff99Frosst/issues/84)). - [Version 1.0.9](https://doi.org/10.5281/zenodo.3256444): Addresses [issue 89](https://github.com/openforcefield/smirnoff99Frosst/issues/89): Fixes torsion t56, where SMIRKS `[!1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4]` should be `[!#1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4]`. The first means "not an isotope with mass 1" (`!1`), but we intend for it to apply to all hydrogens, so it has been changed to `!#1`. + **Not yet in a version**: +- Version 1.0.10: Fixes some issues with FF hierarchy, SMIRKS patterns. Full details available in [openforcefield/openforcefield Issue 367](https://github.com/openforcefield/openforcefield/issues/367). + ## Contributors -Contributors to the relevant .offxml file include: +Contributors to the relevant .offxml files include: - Christopher I. Bayly (OpenEye Software/UC Irvine) - Caitlin C. Bannan (UC Irvine) - David L. Mobley (UC Irvine) diff --git a/smirnoff99frosst/offxml/smirnoff99Frosst-1.0.10.offxml b/smirnoff99frosst/offxml/smirnoff99Frosst-1.0.10.offxml new file mode 100644 index 0000000..13ddb78 --- /dev/null +++ b/smirnoff99frosst/offxml/smirnoff99Frosst-1.0.10.offxml @@ -0,0 +1,339 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 6311da9a9be9a88e0cfb7ddbab6932f50eaccec3 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Thu, 25 Jul 2019 11:51:16 -0700 Subject: [PATCH 2/5] rename 1.0.10 to 1.1.0, xfer comments to 1.1.0, update README --- README.md | 22 ++++++++++++++----- ...0.offxml => smirnoff99Frosst-1.1.0.offxml} | 7 +++++- 2 files changed, 23 insertions(+), 6 deletions(-) rename smirnoff99frosst/offxml/{smirnoff99Frosst-1.0.10.offxml => smirnoff99Frosst-1.1.0.offxml} (98%) diff --git a/README.md b/README.md index 5752f34..d0f91c5 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ DOIs for each force field in this repository can be found in the following table | Filename | DOI | | -------- | --- | -| smirnoff99Frosst-1.0.10.offxml | No DOI yet | +| smirnoff99Frosst-1.1.0.offxml | No DOI yet | | smirnoff99Frosst-1.0.9.offxml | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3256444.svg)](https://doi.org/10.5281/zenodo.3256444) | | smirnoff99Frosst-1.0.8.offxml | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2565295.svg)](https://doi.org/10.5281/zenodo.2565295) | | smirnoff99Frosst-1.0.7.offxml | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1186466.svg)](https://doi.org/10.5281/zenodo.1186466) | @@ -90,6 +90,19 @@ We expect to continue to manually expand this to cover more chemical space and, Subsequent versions are expected to build on Bayly's hand created version with some enhancements by Caitlin Bannan by improving specific parameters, further differentiating some chemical functionality, etc. However, derivatives are expected to retain this basic structure and the AMBER legacy/history; a full refitting of bonded parameters would result in a separate force field rather than a new version of this force field. +In general, this repository will only contain force fields that aim to reproduce the behavior of parm99/parm@Frosst using the SMIRNOFF format. +Once the Open Force Field Initiative begins parameter optimizations, the resulting force field should be migrated to separate base name. + +## General versioning guidelines + +_Applicable in general to SMIRNOFF-format FFs produced by the Open Force Field Consortium_ + +Force fields moving forward will be called `name-X.Y.Z` + +* `X` denotes some major change in functional form. +* `Y` is the parameterization epoch / generation, or a minor change that can affect energy. +* `Z` is a bugfix version -- e.g. something we've caught and corrected. + ## Using SMIRNOFF99Frosst In OpenMM, application of SMIRNOFF99Frosst to small molecules should be straightforward via `openforcefield` with examples available in the [openforcefield repository](https://github.com/openforcefield/openforcefield/tree/master/examples). @@ -106,10 +119,7 @@ Additionally, with ParmEd, it should be possible to convert parameterized OpenMM - [Version 1.0.7](https://dx.doi.org/10.5281/zenodo.1186466): Add hydroxyl hydrogen radii (as per SMIRNOFF initial paper); remove generics with pure wildcards (not even elemental types). - [Version 1.0.8](http://doi.org/10.5281/zenodo.2565295): Fix human error in hydroxyl hydrogens; fix bond parameters between hydrogen and divalent carbons ([issue #81](https://github.com/openforcefield/smirnoff99Frosst/issues/81)); and fixed SMIRKS patterns for angle parameters around trivalent carbon in 5-membered rings ([issue #84](https://github.com/openforcefield/smirnoff99Frosst/issues/84)). - [Version 1.0.9](https://doi.org/10.5281/zenodo.3256444): Addresses [issue 89](https://github.com/openforcefield/smirnoff99Frosst/issues/89): Fixes torsion t56, where SMIRKS `[!1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4]` should be `[!#1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4]`. The first means "not an isotope with mass 1" (`!1`), but we intend for it to apply to all hydrogens, so it has been changed to `!#1`. - -**Not yet in a version**: - -- Version 1.0.10: Fixes some issues with FF hierarchy, SMIRKS patterns. Full details available in [openforcefield/openforcefield Issue 367](https://github.com/openforcefield/openforcefield/issues/367). +- Version 1.1.0: Adds hydrogen bond constraints. Updates contents to SMIRNOFF 0.3 spec (spec change performed by OFF toolkit 0.4.0 reading smirnoff99Frosst-1.0.9, and then writing the `ForceField` object out in the 0.3 spec). Fixes several issues with FF hierarchy, SMIRKS patterns. Full details available in [openforcefield/openforcefield Issue 367](https://github.com/openforcefield/openforcefield/issues/367). ## Contributors @@ -120,6 +130,8 @@ Contributors to the relevant .offxml files include: Special thanks go to John D. Chodera (MSKCC) for his initial implementation of `openforcefield` toolkits and the SMIRNOFF format. +Andrea Rizzi (MSKCC) and Jeff Wagner (OFF/UC Irvine) contributed to the Python and Conda infrastructure of this package. + #### Acknowledgements Project based on the diff --git a/smirnoff99frosst/offxml/smirnoff99Frosst-1.0.10.offxml b/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml similarity index 98% rename from smirnoff99frosst/offxml/smirnoff99Frosst-1.0.10.offxml rename to smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml index 13ddb78..72924b7 100644 --- a/smirnoff99frosst/offxml/smirnoff99Frosst-1.0.10.offxml +++ b/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml @@ -1,10 +1,13 @@ - + C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine; J. R. Wagner, Open Force Field/UC Irvine + Date: July 25, 2019 + + @@ -93,6 +96,7 @@ + @@ -297,6 +301,7 @@ + From 62711f56c26b3eca2b9b91e1c52659e4e9ba1959 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Thu, 25 Jul 2019 14:00:24 -0700 Subject: [PATCH 3/5] Make indentation in constraints section consistent --- smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml b/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml index 72924b7..6817575 100644 --- a/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml +++ b/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml @@ -3,8 +3,8 @@ C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine; J. R. Wagner, Open Force Field/UC Irvine Date: July 25, 2019 - - + + From 65ac11ead13fb12885c45a3801990559bc99d395 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Thu, 25 Jul 2019 14:21:07 -0700 Subject: [PATCH 4/5] tabs to spaces --- .../offxml/smirnoff99Frosst-1.1.0.offxml | 662 +++++++++--------- 1 file changed, 331 insertions(+), 331 deletions(-) diff --git a/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml b/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml index 6817575..e82c84f 100644 --- a/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml +++ b/smirnoff99frosst/offxml/smirnoff99Frosst-1.1.0.offxml @@ -8,337 +8,337 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 0f29c7947fcd2ef1dd4fd426f6dce99bc9e5f28a Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Thu, 25 Jul 2019 15:57:56 -0700 Subject: [PATCH 5/5] add more details about 1.1.0 to README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d0f91c5..8503e38 100644 --- a/README.md +++ b/README.md @@ -119,7 +119,7 @@ Additionally, with ParmEd, it should be possible to convert parameterized OpenMM - [Version 1.0.7](https://dx.doi.org/10.5281/zenodo.1186466): Add hydroxyl hydrogen radii (as per SMIRNOFF initial paper); remove generics with pure wildcards (not even elemental types). - [Version 1.0.8](http://doi.org/10.5281/zenodo.2565295): Fix human error in hydroxyl hydrogens; fix bond parameters between hydrogen and divalent carbons ([issue #81](https://github.com/openforcefield/smirnoff99Frosst/issues/81)); and fixed SMIRKS patterns for angle parameters around trivalent carbon in 5-membered rings ([issue #84](https://github.com/openforcefield/smirnoff99Frosst/issues/84)). - [Version 1.0.9](https://doi.org/10.5281/zenodo.3256444): Addresses [issue 89](https://github.com/openforcefield/smirnoff99Frosst/issues/89): Fixes torsion t56, where SMIRKS `[!1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4]` should be `[!#1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4]`. The first means "not an isotope with mass 1" (`!1`), but we intend for it to apply to all hydrogens, so it has been changed to `!#1`. -- Version 1.1.0: Adds hydrogen bond constraints. Updates contents to SMIRNOFF 0.3 spec (spec change performed by OFF toolkit 0.4.0 reading smirnoff99Frosst-1.0.9, and then writing the `ForceField` object out in the 0.3 spec). Fixes several issues with FF hierarchy, SMIRKS patterns. Full details available in [openforcefield/openforcefield Issue 367](https://github.com/openforcefield/openforcefield/issues/367). +- Version 1.1.0: Adds hydrogen bond constraints. Updates contents to SMIRNOFF 0.3 spec (spec change performed by OFF toolkit 0.4.0 reading smirnoff99Frosst-1.0.9, and then writing the `ForceField` object out in the 0.3 spec). Fixes several issues with FF hierarchy, SMIRKS patterns. This fixes some issues with coverage of certain areas of chemical space, and parameters which could never be utilized due to hierarchy issues. Full details available in [openforcefield/openforcefield Issue 367](https://github.com/openforcefield/openforcefield/issues/367). ## Contributors