pdb2gmx should warn about missing residues when bonds are too long
When residues are missing from input files,
pdb2gmx can blindly generate peptide bonds that are unphysical. This mysteriously breaks later in
pdb2gmx should check that bonds are within a reasonable margin of the equilibrium length - 20%? If they aren't, the warning should hint about missing residues. Obviously,
-maxwarn can get around this check.
#2 Updated by Erik Lindahl about 5 years ago
I think it's time to kill pdb2gmx in its current form instead :-)
Ideally, I would prefer to replace it with two separate tools:
1) A general cleaner tool that can build missing atoms, sidechains, and warn about things that might not be correct with your structure. This one should also set the specific protonation states, termini, and all other biological information you want to embed.
2) A simple tool that takes a perfect input file with every single atom present (see 1) and merely creates a topology for it.
The one thing that would fall somewhat between chairs is the virtual sites, but for those my ideal solution would be to have them as a run-time option in mdrun, just as we can enable/disable constraints.