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10 changes: 5 additions & 5 deletions docs/source/getting_started.rst
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Expand Up @@ -5,7 +5,7 @@ This page details how to get started with *PolyConstruct*.

The design, testing, and validation of *PolyConstruct* is detailed in the manuscript *"PolyConstruct:
adapting biomolecular simulation pipelines for polymers with PolyBuild, PolyConf and PolyTop"*, by
**Rangika Munaweera**, **Ada Quinn**, Luna Morrow, Richard A Morris, and Megan L O’Mara*
*Rangika Munaweera, Ada Quinn, Luna Morrow, Richard A Morris, and Megan L O’Mara*


**Installing PolyConstruct:**
Expand Down Expand Up @@ -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 <https://atb.uq.edu.au>`,
`antechamber <https://ambermd.org/antechamber/ac.html>`, and `LigParGen https://zarbi.chem.yale.edu/ligpargen/`.
exist for small molecule parameterization such as the `Automated Topology Builder <https://atb.uq.edu.au>_`,
`antechamber <https://ambermd.org/antechamber/ac.html>_`, and `LigParGen https://zarbi.chem.yale.edu/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,
Expand Down Expand Up @@ -327,8 +327,8 @@ Complex example - construction of a 4-arm PEG star polymer from single monomeric

Find the above and additional worked examples as executable Python scripts on the `PolyConstruct GitHub repository <https://github.com/OMaraLab/polyconstruct>`_.

Examples for *PolyTop* are available at 'polyconstruct/polytop_examples/'
Examples for *PolyTop* are available at `polyconstruct/polytop_examples/`

Examples for *PolyConf* at 'polyconstruct/polyconf_examples/'
Examples for *PolyConf* at `polyconstruct/polyconf_examples/`

Instructions to use *PolyBuild* are included under the :ref:`PolyBuild` documentation.