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 Extensions → Modeling; 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.
