Topolbuild 1.2

Reads a Tripos .mol2 file with charges to generate something approximating gromacs .gro, .top, and .itp files from it based on selected force field parameters.  Now includes some support for united atom force fields.  Includes tables to support amber, gaff, glycam, and gmx type force fields. Requires that the .mol2 file have syntactically correct Tripos atom types and absolutely will not work with other input atom types.  Includes capability of pruning dihedral angles to a possibly more reasonable set.

Revisions include:

1. Corrected improper dihedrals determination.
2. Added gromacs united atoms force fields, along with some required atom type definition files and parameters files.  Atom type definition files and parameter files are included for gmx43a1, gmx43a2, gmx43b1, gmx45a3, gmx53a5, and gmx53a6.  Only the table for gmx53a6 has received any checking.  All of these tables are incomplete and to be considered experimental.  As with any automatic system for parameterization, careful examination and editing of the results is required to generate a well behaved final topology.
3. Added glycam force fields option and ATOMTYPE_GLYCAM.DEF.  The glycam option is experimental and may not give a correct result.
4. Added option to prune excess dihedral angles.
5. Added conversion of some ring planarity dihedral angles to be output in the topology as improper dihedral angles.
6. Added an internal adjustment to correct for the problem of programs other than Sybyl generating larger charges than those from the standard Sybyl residue dictionary and charge generation methods.
7. Altered topology outputs to allow for various types of bond, angle, and dihedral angle parameters.
8. Made changes to antechamber data tables to correct for problems related to gromacs case insensitivity and for the absence of some atom type combinations in the force field parameters.