/************************************************************************
 *                                                                      *
 *  alchemify  -- Beta Version                                          *
 *                                                                      *
 *  prepare an X-PLOR PSF file for alchemical FEP transformations :     *
 *  - remove parameters (bonds, angles, dihedrals & impropers)          *
 *  coupling the initial and final groups                               *
 *  - add exclusions between all the atoms of the initial group         *
 *  and those of the final group                                        *
 *                                                                      *
 * (C) Jrme Hnin <jerome.henin@uhp-nancy.fr>, March 2004             *
 * This program is distributed under the GNU General Public License     *
 * (see http://www.gnu.org/copyleft/gpl.html)                           *
 ************************************************************************/

How to make a dual-topology alchemical setup using alchemify :

* Generate an X-PLOR PSF containing the dual topology, using either
psfgen,or CHARMM, or any other tool. This PSF may contain auto-generated
angles and dihedrals, you don't have to worry about these. The
unavoidable part of the work is to define the dual topology
more or less by hand, unless the alchemical transformation affects
only whole molecules and not parts of them.

* Create an "FEPfile", that is, a PDB file for your system with a
column (X, Y, Z, O or B) containing 1 for atoms that appear and
-1 for atoms that disappear.

* Run "alchemify input.psf output.psf FEPfile", adding the name of
the FEP column as a last parameter (if it is not B).

* Please send bug reports and suggestions to the author
