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Merge pull request #91 from OMaraLab/recombinatrix-patch-7
Update getting_started.rst
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@@ -84,8 +84,8 @@ Monomer design
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For both *PolyBuild* and *PolyTop*, monomer parameters should include all monomer atoms that will be present
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in the simulation model of the final polymer, and dummy atoms correesponding to connectivity with adjacent monomers.
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The method for preparing monomer .itp depends on the choice of force field, and a number of suitable automated tools
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exist for small molecule parameterization such as the `Automated Topology Builder <https://atb.uq.edu.au>_`,
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`antechamber <https://ambermd.org/antechamber/ac.html>_`, and `LigParGen https://zarbi.chem.yale.edu/ligpargen/_`.
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exist for small molecule parameterization such as the `Automated Topology Builder <https://atb.uq.edu.au>`_,
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`antechamber <https://ambermd.org/antechamber/ac.html>`_, and `LigParGen <https://zarbi.chem.yale.edu/ligpargen/>`_.
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Monomer coordinates and parameters used as inputs should be designed to reflect the state of the monomer
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in the mature polymer chain, rather than the isolated monomer molecule prior to polymerization. For example,

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