Virtual sites in residues

I’ve written a script to take individual .itp files and corresponding .pdb files and insert Hunter-Sanders dummy atoms over the aromatic atoms and appropriately reindex the input files. It requires my bioinf library be cloned to your PYTHONPATH.

Note that currently the virtual charges are independent of each atom’s pi charge, which still needs to be calculated ab initio and updated in the hard-coded dictionary in the script.

Note that the version of Gromos I’m using is a combination of those of Marzouli and the ATB. Essentially a patch from the diff between ATB’s gromos and that packaged with gromacs is applied to that of Marzouli. I also made the DUM atom V type instead of A.

Note that I had trouble using the [ virtual_sites1 ] directive so I used [ virtual_sitesn ] to create the coincident, positively charged virtual sites.