CCL: New information about AmberFFC

 Sent to CCL by: FyD [fyd+*]
 Dear All,
 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
 Regards, Francois
  * F.-Y. Dupradeau *
 DMAG EA 3901 & Faculte de Pharmacie, Amiens, France