From acd1b874f34107f2f0ac2e47c8dc76de50320b18 Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 12:00:04 +1100 Subject: [PATCH] Update getting_started.rst Documentation change didn't populate --- docs/source/getting_started.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index b722986..8ef8fb0 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -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:** @@ -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 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, @@ -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 `_. -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.