An X-PLOR PSF post-processor for alchemical free energy calculations in
Written by Jérôme Hénin
Version 1.4 (June 2009) - tiny fix to handle PSF-CMAP files properly.
As of NAMD 2.7b2, alchemify is not needed anymore, since all unwanted
terms are discarded by NAMD at runtime. At this point, however, this
does not apply to NAMD binaries compiled with the memory optimized
NAMD features an implementation
of alchemical FEP that uses the dual topology approach. Dual topology
requires that the initial and final groups do not interact. To prevent
such interactions, the PSF file describing the system should:
Psfgen is not designed to handle nonbonded exclusion lists, and it is
not straightforward to use it for removing unwanted bonded terms.
Alchemify is a small
program that takes care of these two tasks with minimal effort from the
- contain no bonded parameter coupling the initial and final groups;
- contain exclusion lists ensuring that no nonbonded interactions
between these groups exist.
For simulating single amino-acid mutations in proteins, the setup can
be handled automatically by the VMD
PSF> <output PSF> <FEPfile> [FEP column]
How to use it
- Generate an X-PLOR PSF file containing the dual topology, using
psfgen, or CHARMM, or any suitable tool. This PSF may contain
auto-generated angles and dihedrals. 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, i.e.
a PDB file for your system with a column (usually the B column)
containing a '1' flag
for atoms that appear and '-1' for atoms that disappear.
- Run alchemify in.psf
Alchemify is Free Software. It is distributed under the GNU General Public
License, version 2.