[Molecularmechanics] Recycling CML

[Pengyu Ren]

Hi Konrad

I just took a quick look at the two proposals by you and David. David's certainly more specific to protein. In your proposal two however each residue/fragment is a "molecule" (why can't we just call it fragment?). It's then easy to make a new molecule by resuing fragment libraries. 

I noticed your concern about definition of fragment, which may be force field dependent. For protein, my suggestion is to use the whole residue as a fragment, which makes interchanging force field a _lot_ easier. For any other new molecules and new force field, whoever develop it should give the definition of fragments and corresponding parameter files in such format. 

It will a diiferent story if one tries to guessed parameters for an abitrary molecule. I think the fragment library is the way to go in the long run.

For protein modeler, I propose we also define a format for paramter file. We only need one copy of it. It should contain all the amber, charmm, ,,, paramters, fuctions in the format corresponding to the structure file format. Any new fuctions/paramters/force field can be added to that file by developer accordingly.

Pengyu