Model building

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Modeller
does homology building.
Dowser
can help you to solvate a protein before simulations.
VMD
comes with a lot of useful modeling tools in ExtensionsModeling; it can auto-build xplor-style psf files, add ions to the system, solvate, mutate, ...
Charmm
has a fairly complete (but as always, idiosyncratic) model building facility with the IC commands.
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