qprep charge groups ambivalent indexing shows no error

[dblahanelson]

I made a topology in qprep using a library that had charge groups containing two H43's and no H42's, e.g. when making charge groups, I accidentally labelled H42 as H43 while also naming H43 as H43. Qprep made that topology with no errors. One should, of course, be more careful. Still, it might be useful if qprep noticed the charge groups made no sense.

[acmnpv]

Hello, if you could upload a test case I could have a look at fixing this, thank you!

[dblahanelson]

In this example, both libraries have atoms H42 and C43 listed in [atoms], neither has an H43 listed.

In [charge_groups], the correct library has H42 in one charge group and C43 in another charge group. The incorrect library has H43 in one charge group, C43 in another charge group and no H42 at all, even though H42 exists and H43 doesn't. Both create topologies successfully and have identical log files.

I propose that charge groups cannot have atoms that aren't listed in [atoms], or that it at least throws an error.

test_case.zip