pdb2gmx does not report why chains of residues are teminated
In find_nc_ter(), the chain is terminated when a residue is found whose type does not match that of the rest of the chain. This happens frequently when users modify a residue and forget to change residuetypes.dat.
We should at least report the reason for the termination, so the user being prompted for a C terminus after the residue before the modified one can see why they are being prompted. Perhaps we should also suggest editing residuetypes.dat when this occurs.
Improve pdb2gmx for nonstandard residue types
If explicit non-blank chain identifiers are set, it
will now be a hard error if the residue types in each
chain do not match. For blank chain ID we still need
to allow detection of non-chain parts, but this case
too now provides more explicit output information.