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 Nov 4, 2013
Email address: vv0210@gmail.com

added support for flags used in current version of AMBER

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

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
