inital draft

[fgrunewald]

Initial draft for converting itps. The current command line interface looks like so:

martini_sour -f <name_of_itp_file> -o <name_of_outfile> -tres <resname: > -pkas <resname: pKa_value>

The tres specification makes use of the vermouth rich syntax, which allows users to tag very specific residues in large molecules if needed. This will be a huge plus for protein stuff, because it allows you to only convert specific residues. For example to convert phenyl-valeric acid from M3 to titratable:

martini_sour conv_itp -f PVA_M3.itp -tres PVA:acid -o titr_PVA.itp -pkas PVA:4.2

There are some hardcoded limitations:

• only 1 titratable side per residue
• names of the beads of the acid/bases have to be named ACD or BAS in the original itp file
• beads connecting to the acid/base have to be part of the same residue and be named R

The last one is easy to work around. The middle one requires some thinking. Probably the user would have to specify the bead-name with the residue.

Currently this branch depends on fixing a bug in vermouth issue 384.

Also we have a very limited set of beads, so it would probably be a good idea to do some filtering of proper input and pKa values. At least for the time being. But that can be done after the chapter is submitted.