Update 01_setup_abfe.ipynb

Author: jmichel80

04_fep/03_ABFE/01_setup_abfe.ipynb

@@ -112,7 +112,7 @@
  "\n",
  "In some ways ABFE calculations are simpler than RBFE calculations, in that we do not need to align and merge two ligands. However, ABFE calculations require receptor-ligand restraints (shown by the red dotted lines above) to prevent sampling issues. To obtain converged free energies of binding without restraints, we would have to be sure that the ligand was sampling outside the binding site as soon as the unbound state became comparable in free energy to the bound state, and that we were correctly estimating the ratios of the sizes of the simulation box to the binding site; in practice, this is not generally feasible.\n",
  "\n",
- "There are several varieties of receptor-ligand restraints, including [distance-to-bound configuration (DBC) restraints](https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b00447), [restraints on coarse variables derived by finding the optimal rotation which minimises the complex's RMSD with respect to a reference structure](https://pubs.acs.org/doi/full/10.1021/acs.jctc.7b00791), and [multiple distance restraints](https://pubs.acs.org/doi/10.1021/acs.jctc.3c00139). We are interested in multiple distance restraints and plan to implement automated multiple distance restraint selection and implementation in BioSimSpace and SOMD in future. \n",
+ "There are several varieties of receptor-ligand restraints, including [distance-to-bound configuration (DBC) restraints](https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b00447), [restraints on coarse variables derived by finding the optimal rotation which minimises the complex's RMSD with respect to a reference structure](https://pubs.acs.org/doi/full/10.1021/acs.jctc.7b00791), and [multiple distance restraints](https://pubs.acs.org/doi/10.1021/acs.jctc.3c00139).\n",
  "\n",
  "Here, we will use the set of receptor-ligand restraints originally proposed by [Boresch et al.](https://pubs.acs.org/doi/full/10.1021/jp0217839), because they are simple to implement, very widely used, and the only restraints currently supported by BioSimSpace. These restrain all 6 relative external degrees of freedom (three translational and three rotational) of the ligand with respect to the receptor. This is done by imposing harmonic restraints on one distance, two angles, and three dihedral angles defined by three anchor points in the protein (P1-3) and three in the ligand (L1-3):\n",
  "\n",