Moltemplate

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

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](https://github.com/jewettaij/moltemplate/blob/master/doc/doc_mol22lt.md)

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.

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.

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!