reverted the "moltemplate.sh" file back to v2.18.8 to fix a packaging bug

This fixed a unit test failure I was having after introducing v2.17.9.

fixed a bug causing trouble on systems with both python2 and python3 installed

v2.17.8

fixed a bug causing trouble on systems with both python2 and python3 …

updated and documented genpoly_modify_lt.py & genpoly_lt.py. added DNA examples

Slight changes were made to the behavior of genpoly_lt.py and genpoly_modify_lt.py. The coarse grained examples have been reorganized. Some complex coarse grained DNA examples have been added or updated.

fixed more bugs in "genpoly_modify_lt.py"

Still no documentation for the "genpoly_modify_lt.py" program yet. (I doubt this program is useful to anyone else yet. But future examples will require it, so I should eventually document what it does.)

fixed a minor bug in genpoly_lt.py

It was not behaving correctly when invoked using the "-box" argument. (The minimum X,Y,Z coordinates were not allowed to exceed 0.)

fixed a bug in "interpolate_curve.py"

The bug was preventing the correct scaling of coordinates when using "interpolate_curve.py". (This bug has no effect unless the "scale" parameter was used.)

fixed a bug preventing wildcards in _coeff commands

Fixed a bug that prevented wildcards in _coeff commands from being interpreted correctly in some files generated moltemplate. Currently, they are ignored unless they appear in the "In Settings" section (<-->"system.in.settings") file. Now all files generated by moltemplate are screened for wildcards in _coeff commands.

fixed a serious bug in cleanup_moltemplate.sh

This is a disturbing and potentially serious bug that causes "cleanup_moltemplate.sh" to alter the order of improper atoms for all force fields, (including GAFF, GAFF2, OPLSAA, and COMPASS). It is unlikely but also possible it could have caused improper interactions to be incorrectly identified as redundant and deleted. Thanks to bhargavchava97 (again) for catching this!

AMBER GAFF bugfix (credit: bhargavchava97)

Important correction to AMBER GAFF and GAFF2 force fields (improper interactions). Prior to this version, molecules built using AMBER force fields (GAFF and GAFF2) would contain redundant improper interactions. This might cause these molecules to be unrealistically stiff. Currently the improper interactions generated by moltemplate now agree with improper interactions generated by AmberTools/Antechamber. (Details: I can't guarantee that the order that the atoms appear in each improper is equivalent, but at least the number of improper interactions is correct, the central atom is correct, and the atoms involved are correct.) This bug fix was contributed by bhargavchava97(github user). THANKS!

added the amberfrcmod2lt.sh converter for AMBER FRCMOD files

Added the "amberfrcmod2lt.sh script for converting user-supplied FRCMOD files into moltemplate LT files that can be used with gaff.lt and gaff2.lt. I will eventually have to document all of the scripts in this directory for them to be useful to end users. (On my to-do list.) I also corrected some some of the error messages in genpoly_lt.py.