diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index 8ef8fb0..771f3b1 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -84,8 +84,8 @@ Monomer design For both *PolyBuild* and *PolyTop*, monomer parameters should include all monomer atoms that will be present in the simulation model of the final polymer, and dummy atoms correesponding to connectivity with adjacent monomers. The method for preparing monomer .itp depends on the choice of force field, and a number of suitable automated tools -exist for small molecule parameterization such as the `Automated Topology Builder _`, -`antechamber _`, and `LigParGen https://zarbi.chem.yale.edu/ligpargen/_`. +exist for small molecule parameterization such as the `Automated Topology Builder `_, +`antechamber `_, and `LigParGen `_. Monomer coordinates and parameters used as inputs should be designed to reflect the state of the monomer in the mature polymer chain, rather than the isolated monomer molecule prior to polymerization. For example,