Update links to SMIRNOFF spec from deleted topology branch

content/faq/_index.md

@@ -36,7 +36,7 @@ We firmly believe that research in this space is not a zero-sum game; with the r
 ## Can we use your software in our force field effort?
 
 Yes! Everything is open source under permissive licenses (generally the MIT License). We are also open to suggestions from the community, as well as community input on the codes and research directions. Please contribute to our GitHub issue trackers for projects at http://github.com/openforcefield, or even feel free to contribute code if you find it useful!
-Our [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html) force field specification is an excellent way to ensure your force field will be portable between many biomolecular simulation packages, and we intend for our tools for force field parameterization to also be widely useful in addressing exciting questions in force field science.
+Our [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html) force field specification is an excellent way to ensure your force field will be portable between many biomolecular simulation packages, and we intend for our tools for force field parameterization to also be widely useful in addressing exciting questions in force field science.
 
 ## Requesting Letters of Collaboration
 

content/forcefields/_index.md

@@ -34,5 +34,5 @@ using the [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/0.3.0/smi
 [[GitHub]](https://github.com/openforcefield/smirnoff99Frosst) |
 [[Download]](https://github.com/openforcefield/smirnoff99Frosst/releases)
 
-*This force field achieves [comparable accuracy to GAFF](https://doi.org/10.1101/286542) in physical properties, but with with a decrease in complexity from over 6000 lines of parameters to only ~300 lines using the SMARTS-based [direct chemical perception](https://doi.org/10.1101/286542) possible with [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html).
+*This force field achieves [comparable accuracy to GAFF](https://doi.org/10.1101/286542) in physical properties, but with with a decrease in complexity from over 6000 lines of parameters to only ~300 lines using the SMARTS-based [direct chemical perception](https://doi.org/10.1101/286542) possible with [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html).
 This force field is intended to be a starting point for rapid cycles of automated optimization to rapidly improve accuracy for modeling protein - small molecule interactions.*

content/news/rdkit-support-is-coming.md

@@ -32,13 +32,13 @@ Initially, we are adding support for the following toolkits:
 * The [RDKit](http://www.rdkit.org), which provides support for molecule reading/writing, conversion to/from SMILES, and SMARTS matching, but does not provide AM1-BCC charge assignment capabilities
 * The [AmberTools](http://ambermd.org/AmberTools.php) for assigning AM1 and AM1-BCC charges via `sqm`
 
-Initially, this means that the RDKit and AmberTools together can provide complete functionality for assignment of [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html) parameters for small molecules.
+Initially, this means that the RDKit and AmberTools together can provide complete functionality for assignment of [SMIRNOFF](https://github.com/openforcefield/openforcefield/blob/e3606e3aa2aefa14123e6179b6ece1cd35cf8f50/The-SMIRNOFF-force-field-format.md) parameters for small molecules.
 We will include automatic installation of both of these toolkits as part of the next `conda` release of the openforcefield toolkit.
 
 ### A new draft SMIRNOFF 1.0 specification
 
 While the [SMIRNOFF 0.1 specification](https://doi.org/10.1101/286542) was a significant step forward in automated chemical perception based force fields, it was incomplete and inconsistent in some ways that would hinder its growth.
-This release will include a new backwards-incompatible [draft SMIRNOFF 1.0 specification](https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html) that will support rapid improvements in force field accuracy over the next year, featuring multiple improvements:
+This release will include a new backwards-incompatible [draft SMIRNOFF 1.0 specification](https://github.com/openforcefield/openforcefield/blob/e3606e3aa2aefa14123e6179b6ece1cd35cf8f50/The-SMIRNOFF-force-field-format.md) that will support rapid improvements in force field accuracy over the next year, featuring multiple improvements:
 
 * Aromaticity model now defaults to `OEAroModel_MDL`, and aromaticity model names drop OpenEye-specific prefixes
 * Top-level tags are now required to specify units for any unit-bearing quantities to avoid the potential for mistakes from implied units.
@@ -64,11 +64,11 @@ This release will include a new backwards-incompatible [draft SMIRNOFF 1.0 speci
 * Eliminated "Requirements" section, since it specified requirements for the software, rather than described an aspect of the SMIRNOFF specification
 * Fractional bond orders are described in `<Bonds>`, since they currently only apply to this term.
 
-The current draft SMIRNOFF 1.0 specification can be found here: [Draft SMIRNOFF 1.0 specification](https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html)
+The current draft SMIRNOFF 1.0 specification can be found here: [Draft SMIRNOFF 1.0 specification](https://github.com/openforcefield/openforcefield/blob/e3606e3aa2aefa14123e6179b6ece1cd35cf8f50/The-SMIRNOFF-force-field-format.md)
 
 ### New openforcefield `Molecule` and `Topology` objects
 
-Specifying the system to parameterize with [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html) previously required passing along a set of OpenEye Toolkit [`OEMol`](https://docs.eyesopen.com/toolkits/python/oechemtk/OEChemClasses/OEMol.html) objects.
+Specifying the system to parameterize with [SMIRNOFF](https://github.com/openforcefield/openforcefield/blob/e3606e3aa2aefa14123e6179b6ece1cd35cf8f50/The-SMIRNOFF-force-field-format.md) previously required passing along a set of OpenEye Toolkit [`OEMol`](https://docs.eyesopen.com/toolkits/python/oechemtk/OEChemClasses/OEMol.html) objects.
 To support the migration toward broader support for fully open source toolkits, we have introduced two new classes intended to aid the reading and manipulation of biomolecular systems for parameterization:
 * [`Molecule`](https://open-forcefield-toolkit.readthedocs.io/en/topology/topology.html#molecule): A simple pure Python class for manipulating molecules and interconverting with different toolkits
 * [`Topology`](https://open-forcefield-toolkit.readthedocs.io/en/topology/topology.html#topology): A simple pure Python class for manipulating collections of molecules to simplify application of parameters

content/news/seeking-nih-funding.md

@@ -22,9 +22,9 @@ You can read the science components of the proposal here: [[PDF]](2019-03-05 Ope
 ![alt text](offc-overview-figure.jpg "Open Force Field Initiative R01 schematic overview of aims")
 
 We are committed to making sure our tools work with a wide variety of popular and high-performance molecular simulation packages, including [gromacs](http://www.gromacs.org/), [OpenMM](http://openmm.org/), [AMBER](ambermd.org), [CHARMM](https://www.charmm.org/), [NAMD](http://www.ks.uiuc.edu/Research/namd/), and [Desmond](https://www.deshawresearch.com/resources_desmond.html).
-While we can't do this alone, we are thrilled to be working with developers of these packages to continue to ensure we can reach the widest audience possible and allow force fields (both Initiative-developed and force fields from others converted to the [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html) specification) to broadly interoperate between packages.
+While we can't do this alone, we are thrilled to be working with developers of these packages to continue to ensure we can reach the widest audience possible and allow force fields (both Initiative-developed and force fields from others converted to the [SMIRNOFF](https://github.com/openforcefield/openforcefield/blob/e3606e3aa2aefa14123e6179b6ece1cd35cf8f50/The-SMIRNOFF-force-field-format.md) specification) to broadly interoperate between packages.
 
 We also aim to support the great variety of exciting force field science explored by multiple force field development communities, and have been working to engage various biomolecular force field communities to ensure we are maximally supportive of their efforts.
-We aim for our tools to provide modern resources to support their scientific innovations, as well as allow the force fields they develop to be used in multiple simulation packages via [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html).
+We aim for our tools to provide modern resources to support their scientific innovations, as well as allow the force fields they develop to be used in multiple simulation packages via [SMIRNOFF](https://github.com/openforcefield/openforcefield/blob/e3606e3aa2aefa14123e6179b6ece1cd35cf8f50/The-SMIRNOFF-force-field-format.md).
 We firmly believe that force field science is *not* a zero-sum game, and that we can increase the utility of biomolecular simulation throughout biology and drug discovery by working together.
 To request a letter of collaboration from the Open Force Field Initiative to help support your application for funding, please see **Requesting a Letter of Collaboration** in our [FAQ](https://openforcefield.org/faq/).