This directory consists of two sets of parameters for all solutes, sorted by solvent, for AMOEBA and GAFF. 

Contents:
AMOEBA
A directory with the AMOEBA parameters and inital coordinates of each solute in a solvent box prepared in TINKER and AMBER format
a)TINKER format defined by:
 (xxx.prm)-	The original amoeba09.prm parameters with the addition of solute and solvent parameters provided at the bottom of file.
		Relevant changes to eg. bond lengths and angles (modified to those of QM geometry optimised structures) 
                have been tagged with "NAM"
 (xxx.xyz)-	An initial set of coordinates of the solute soaked in a solvent box in TINKER xyz format.

b)AMBER format defined by:
 (xxx.prmtop)-	The above parameters in AMBER format generated using the tinker_to_amber utility of AMBER14.
		This is provided for all solutes except solutes and solvents with Z-bisector multiple local frame assigment
		(DMSO, acetonitrile, methylamine and trimethylamine). 
 (xxx.inpcrd)-	An inital set of coordinates of the solute soaked in a solvent box in AMBER coordinate format.


GAFF
A directory with the GAFF parameters for all solutes and solvents. 
a)Solute parameters defined by:
 (xxx.frcmod)&-	Parameters generated using the ANTECHAMBER program in AMBER 14 implementing AM1-BCC atomic charges.
 (xxx.prepi) 
 
b)Solvent parameters defined by: 
 (xxx.frcmod)/-	Existing solvent box parameters taken from the AMBER parameter database at http://sites.pharmacy.manchester.ac.uk/bryce/amber/
 (xxx.off)

Noor Asidah Mohamed, Richard Bradshaw & Jonathan Essex, July 2016
