CCL: New information about AmberFFC
- From: FyD <fyd+*+u-picardie.fr>
- Subject: CCL: New information about AmberFFC
- Date: Wed, 14 Sep 2005 12:18:36 +0200
Sent to CCL by: FyD [fyd+*+u-picardie.fr]
Description of AmberFFC
A program for converting the different existing AMBER and GLYCAM force fields
for use with commercial molecular modeling packages is presented, using the
Molecular Simulations Inc. (MSI or Accelrys) software package as a case model.
Called AmberFFC, the program creates AMBER and GLYCAM force field files
suitable for use with the Accelrys molecular mechanics modules by transforming
the amino acid, nucleotide, and monosaccharide topology databases and force
field parameter files to the Accelrys file format. It is intended for any
modeler who is interested in using the current AMBER and GLYCAM force fields
with the Accelrys FDiscover and CDiscover programs. AmberFFC has been written
entirely with the Perl programming language, making it highly flexible and
portable. In order to compare the implementation of the force fields converted
by AmberFFC in the Accelrys package with their corresponding execution in the
AMBER software, and also to verify the efficiency of the AmberFFC program,
results from single point energy calculations for 13 model molecules were
obtained with the two programs. It is demonstrated that results obtained with
the CDiscover and FDiscover modules compare well to those found using
Sander_classic, thus showing that AmberFFC is a highly efficient program. Some
energy differences between the AMBER and Accelrys software have been observed,
and their origin has been characterized and discussed.
New information for AmberFFC users from Accelrys Inc.
There were bugs in the CDiscover (Discover_3) module making the energy values
obtained with CDiscover & the AMBER force fields (converted by AmberFFC)
erroneous. After 4 years or so, Accelrys Inc. just provided a bug correction
which makes the use of AMBER force fields in Discover fully effective.
For more information, see the AmberFFC web site
* F.-Y. Dupradeau *
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France