Merge pull request #476 from openforcefield/amber_swap

This adds an example of swapping SMIRNOFF for GAFF parameters for a protein-ligand complex

Author: j-wags

examples/README.md

@@ -7,6 +7,7 @@ The following examples are available in [the openforcefield toolkit repository](
 * [SMIRNOFF_simulation](https://github.com/openforcefield/openforcefield/tree/master/examples/SMIRNOFF_simulation) - simulation of a molecule in the gas phase with the SMIRNOFF forcefield format
 * [forcefield_modification](https://github.com/openforcefield/openforcefield/tree/master/examples/forcefield_modification) - modify forcefield parameters and evaluate how system energy changes
 * [using_smirnoff_in_amber_or_gromacs](https://github.com/openforcefield/openforcefield/tree/master/examples/using_smirnoff_in_amber_or_gromacs) - convert a System generated with the Open Forcefield Toolkit, which can be simulated natively with OpenMM, into AMBER prmtop/inpcrd and GROMACS top/gro input files through the ParmEd library.
+* [swap_amber_parameters](https://github.com/openforcefield/openforcefield/tree/master/examples/swap_amber_parameters) - take a prepared AMBER protein-ligand system (prmtop and crd) along with a structure file of the ligand, and replace ligand parameters with OpenFF parameters.
 * [inspect_assigned_parameters](https://github.com/openforcefield/openforcefield/tree/master/examples/inspect_assigned_parameters) - check which parameters are used in which molecules and generate parameter usage statistics.
 * [using_smirnoff_with_amber_protein_forcefield](https://github.com/openforcefield/openforcefield/tree/master/examples/using_smirnoff_with_amber_protein_forcefield) - use SMIRNOFF parameters for small molecules in combination with more conventional force fields for proteins and other components of your system (using ParmEd to combine parameterized structures)
 * [check_dataset_parameter_coverage](https://github.com/openforcefield/openforcefield/tree/master/examples/check_dataset_parameter_coverage) - shows how to use the Open Force Field Toolkit to ingest a dataset of molecules, and generate a report summarizing any chemistry that can not be parameterized.

examples/swap_amber_parameters/README.md

@@ -0,0 +1,8 @@
+## Taking an AMBER system and replacing the ligand parameters with OpenFF parameters
+
+These examples illustrate how the [ParmEd](http://parmed.github.io/ParmEd/html/index.html) utility can be used to take a fully parameterized (and solvated) protein-ligand system and replace the ligand parameters with those from OpenFF. In this case, the system uses an AMBER protein force field, ions, and TIP3P water, and we replace the GAFF ligand parameters with OpenFF 1.0 parameters, writing out the resulting fully parameterized system.
+
+### BRD4:inhibitor complex
+
+
+[`swap_existing_ligand_parameters.ipynb`](swap_existing_ligand_parameters.ipynb) contains an example illustrating taking a fully parameterized BRD4 protein-ligand system, with an AMBER protein force field and GAFF ligand parameters, and replacing the ligand parameters with OpenFF parameters from SMIRNOFF format. The BRD4:inhibitor complex is taken from the [free energy benchmark systems living review](https://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-070816-033654) [GitHub repo](https://github.com/MobleyLab/benchmarksets/tree/master/input_files/BRD4).