[BUG] create_from_pertfile uses next instead of continue when skipping atoms that don't match the perturbation template

[lohedges]

When matching atoms to the perturbation template the current code incorrectly uses next to skip the atom in the case of a mismatch (see here). This will raise cause an Exception to be raised if the first atom in the molecule isn't in the atoms section of the pert file, i.e. it is unperturbed. However, if there is a later mismatch, then the wrong values of the end state charge,LJ, and ambertype will be applied to the atom. The solution is to replace next with continue.

[lohedges]

On a related not, I'm not sure if the error message that is printed when the atom is skipped is too useful. (Perhaps this is for debugging.) Since the atom records in the pert file only contains perturbing atoms, there will likely be many situations where atoms in the topology aren't matched. Perhaps there could be a verbose mode that prints what did and didn't match so that the user can cross-reference if they wish?

[chryswoods]

Thanks - good catch :-)

Yes, that error message was left over from debugging. I'll remove it and will then merge into devel.