new tool for AmberTools 'tleap'

[thepineapplepirate]

This is a new tool for the AmberTools program "tleap". This tool will fulfill many needs, including now having full access to the newer AMBER force fields, and other specialized forcefields (metalloprotein forcefields like ZAFF and EZAFF, for example), which are not in the GROMACS source code. By generating these files with tLeap, and then processing the outputs with acpype, these newer features can successfully be used with MD simulations conducted in Galaxy/GROMACS.

[thepineapplepirate]

Hey @bgruening,

thanks for the thorough review! I'm going to go over some things and come up with a new draft addressing some issues, particularly what should be a macro and what shouldn't. I will inform you guys when the new draft is pushed back and ready for review. Thanks again for your time and effort with this and the other PRs :).

-BR

[bgruening]

Cool, thanks!

[thepineapplepirate]

• would it be useful to also test for the consistency of tleap_in ? I mean that the content is as expected?

added a 'lines_diff' and a reference stock file (leap_testfile.txt) in test-data/ to verify consistency in the produced config file