ProtoMS is a complete Monte Carlo biomolecular simulation program designed to calculate relative free energies (including relative binding free energies) on large systems. It supports FEP, FDTI, RETI, umbrella sampling, and can run using large system (hundreds of thousands of atoms), using either explicit water models or the implicit GBSA water model.
ProtoMS has been used to produce the science in multiple publications. This website is being constructed to support the future development of the code, and support its continued use. We are only now beginning to create this website, so please be patient while we move everything online.
If you want to download ProtoMS, please visit protoms.googlecode.com and either download either a released version (from the "Downloads" section) or feel free to download a (possibly broken!) version from the subversion repository.
ProtoMS comes with a tutorial (in the "tutorials" directory, file ProtoMS.htm). A copy of this tutorial can also be found here. ProtoMS was also used in a workshop teaching how to calculate relative hydration and binding free energies. The workshop, together with all materials, can be found here.
If you want to ask questions or get help, then please join the ProtoMS Users mailing group.