			These Python scripts were written originally by Keir Novik, but he can
			no longer support them. See some documentation at the top of the
			files - they are supposed to be fairly self-explanatory.

			amber2lammps.py converts AMBER files into LAMMPS input format
			dump2trj.py converts LAMMPS dump files into AMBER format
			dump2try99.py same as dump2trj for LAMMPS 99 format

			-------------------------

			Modifications in file amber2lammps.py, by Vikas Varshney
			Dated July 5, 2005
			Email address : vv5@uakron.edu

			Lines 222-226: Undid the shifting of the atoms in the periodic
			box. LAMMPS is going to take care of it by image atoms. Make sure that
			when you dump the coordinates by LAMMPS to view in VMD, print them in
			the format mentioned in the dump2ptraj.py section later.

			Lines 378-391: Added an if statement to see whether .crd or .top file
			is being read. This if statement helps in assigning the title if the
			title is not present in the files.

			Line 394: Added an if statement, not to read lines which start with
			% in the topology file.

			Lines 430-432: Changed if statement condition to read the current
			simulation time from .crd file. I put the remainder condition
			instead of equal to condition. The simulation time adds one value to
			the length of the Item_list, so remainder condition can be applied
			easily to see if simulation time data is present in the .crd file or
			not.

			In general, the initial .crd files dont have simulation time
			information while restart files do have them.

			Some other minor additions:

			I added few lines to print the names which are being read
			currently. This helps in seeing current state of the programs which
			are listed below

			Lines 382, 389, 420, 428, 436, 490, 498, 550, 555, 560, 565, 570, 575,
			580, 595, 600, 610, 615, 620, 631, 636, 648, 657, 666, 677, 688, 701,
			720, 725, 730, 735, 740, 745, 750, 755, 767, 769, 771, 778, 785, 806,
			821, 897.

			---------------------------

			Modifications in file dump2trj.py, by Vikas Varshney
			Dated July 5, 2005
			Email address: vv5@uakron.edu

			First, the atoms should be dumped in the following format.

			dump group-ID custom N tag type xs ys zs ix iy iz

			Modifications:

			Lines 117-119: I modified the lines to get the actual co-ordinates
			instead of box coordinates. If we dont do that and try to see the
			file in vmd, we observe long bond lengths of the molecules whose one
			part is on one side of periodic box and the other part is on other
			side of periodic box.

			Lines 239 & 244: Changed x to mdcrd.

			Once you do that. Open the original topology file in VMD (with parm7)
			and then mdcrd file (crdbox) to see the time evaluation of the
			problem.

			----------------------------

			Example input script, by Paul Crozier
			1 Sept 2005

			Here is an example of a typical LAMMPS input script for use with
			a data file built by amber2lammps.py:

			units real
			neigh_modify delay 5 every 1
			atom_style full
			bond_style harmonic
			angle_style harmonic
			dihedral_style harmonic
			pair_style lj/cut/coul/long 10.0
			pair_modify mix arithmetic
			kspace_style pppm 1e-4
			read_data data.yourdata
			fix 1 all nve
			special_bonds amber
			thermo 1
			thermo_style multi
			timestep 0.5
			run 2

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