A tool to set up alchemical FEP transformations

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Mon Mar 29 2004 - 10:27:12 CST

Hi all,

I've written a small tool to help for the preparation of X-PLOR PSF files for
alchemical transformations. The aim is to make dual-topology setups a bit
easier, and to make them possible using only psfgen.

Using this, you shouldn't need to worry about auto-generated angles and
dihedrals coupling both ends of the transformation, since the program removes
them. It also generates the exclusion lists required to prevent non-bonded
interaction between the appearing and vanishing atoms.

It simply works as a post-processor for an existing PSF file, typically built
with psfgen or CHARMM. It also needs a FEPfile (as described in the NAMD
manual), stating what atoms belong to the initial and final groups. Given
these, the tool produces a cleaned-up PSF file, that should be suitable for
alchemical FEP with NAMD.

Since this is a preliminary version, I'd like people to test it on their own
systems and report any problems they encounter. Suggestions for improvement
of all kinds are welcome.

Source code is attached, as well as Linux x86 and SGI IRIX64 binaries, and a
README file.

Jérôme Hénin
Equipe Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS    UMR 7565
B.P. 239	54506 Vandoeuvre-lès-Nancy Cedex
Tel : (33) 3 83 68 43 95	Fax : (33) 3 83 68 43 71

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