updated GAFF2, amber2lt.py, and a few alkane examples

The @atom:hw and @atom:ow atom types in "gaff2.lt" now have been given epsilon and sigma parameters (of 0.0 and 1.0). These parameters are not correct, but at least users who don't need these atom types and want to use "gaff2.lt" will be able to do so (without LAMMPS complaining about missing pair_coeffs).

Similarly the amber2lt.py program will now supply default epsilon and sigma parameters (of 0.0 and 1.0) for atoms when this information is lacking in the FRCMOD or DAT file containing the force-field parameters (such as "gaff2.dat").

The amber2lt.py program accepts a slightly wider range of FRCMOD file formats.

Thanks to Karteek Bejegam and Jonathan Campeggio for their debugging help and suggestions!

added the amber2lt.py conversion tool

The newly added amber2lt.py program converts force-field files used by and created by AmberTools (such as FRCMOD and DAT files) into moltemplate (LT) format. The "gaff.lt" and "gaff2.lt" files were created with this program. Now users can use this tool as well with their own custom FRCMOD files.

The amber2lt.py script replaces amberparm_.py files and amber.sh scripts that were used before. (Those scripts were buggy and undocumented.)

fixed a bug in moll22lt.py

Fixed a bug in mol22lt.py which occurs when the subID numbers in the MOL2 file do not begin at 1. (In the past, I had only tested it on files where the subunit ID begins at 1.)

mol22lt.py and documentation improvements

mol22lt.py now creates less confusing LT files when the MOL2 file contains only a single subunit.
Additional improvements to the documentation were also made.

fixed a small bug in mol22lt.py

The "--charges" argument for mol22lt.py should be working now.

I forgot to mention that the AMBER "gaff.lt" and "gaff2.lt" files were also recently updated today (in moltemplate v2.20.8). This should help a lot of people who use GAFF or GAFF2.

I also made some minor improvements to the
mol22lt.py documentation

initial (alpha) attempt at MOL2 file conversion

The new converter program (mol22lt.py) converts MOL2 files to moltemplate (LT) files. This program has not been widely tested and probably fails on some MOL2 files. But the program appears to be useful in some cases.

I fear it is possible I have misinterpreted the MOL2 file format when I wrote this converter. Once I this feature has been tested on a wider variety of MOL2 files, I'll post another version update.

bugfix: stop deleting the "system.in" file

This is a very minor update, but I thought it was important. Some people edit that file, and their work was getting erased.
Thanks again to Jordan Dialpuri for catching this bug.

renamed the "system.in" file to "run.in.EXAMPLE"

I also removed the "moltemplate_manual.pdf" file because it was causing the .git directory to grow in size rapidly as I made frequent changes to this large binary file.

Thanks to Jordan Dialpuri for the suggestion!

fixed a bug when using "@{atom:NAME}" syntax

fixed a bug that occurs when @{atom:NAME} syntax is used inside pair_coeff commands. (The explicit use of {} brackets was sometimes failing.)

Thanks to Otello Roscioni (MaterialX, LTD, https://materialx.co.uk) for reporting the bug!

updated the LOPLS force field file ("loplsaa.lt")

The new version of "loplsaa.lt" includes much more clear atom type descriptions (for the atoms described in the 2015 LOPLS paper, at least).

I also removed some (hopefully) unnecessary and confusing atom types (such as 81LL, 118L, 718LL).

The moltemplate.sh program has not been modified, but I updated the version info anyway. (I had to change the version number of the project in order to be able to upload a new version to pypi.)

Please let me know if I have made any mistakes in the process.
-Andrew