Modularize pdb2gmx

From wiki.gromacs.org

pdb2gmx is a monstrous program that usually works. It currently is very messy and therefore hard to modify it. What needs to be done is to break it up in modules that can be used as separate programs but also as part of a larger program. The same goes to some extent for grompp, and there is a separate project to take the virtual sites out of both grompp and pdb2gmx, see Genvsites. A possible break-up could be:

 Cleanpdb - read coordinate file (pdb/gro/...) and clean it up, that is add missing atoms, rename according to IUPAC/IUPAB recommendations
 Pdb2top  - read a correct coordinate file and generate a top file
 Genvsites - read a top and coordinate file and generate new top and coordinate file with virtual sites
 Gentpr - read a top, coordinate and mdp files and generate a self-contained input file for mdrun

It should also be possible to run mdrun straight from a pdb file. At first this can be done using a script (since we may need to run genbox and genion as well). Eventually one would like to be able to have certain (user-defined) MD protocols which take care of everything, including minimization, restrained equilibration and production.