Based on the force field (FF) requested in the 'System.config' file (keyword 'FFPARM', and see the list of handled force fields), the PyRED program generates three different 'frcmod' files, which contain FF parameters in the Amber file format. These files list and provide the FF parameters required to study the input molecule(s) of the PyRED job (and its corresponding fragments) by molecular dynamics (MD) simulation.
        A script is also produced to load and use the FF libraries and FF parameter files generated by PyRED in the LEaP program (AmberTools).

      -1- The frcmod.known file
      -2- The frcmod.correspondence file
      -3- The frcmod.unknown file
      -4- The LEaP script

    -1- The frcmod.known file

• The 'frcmod.known' file reports FF parameters required to study the PyRED input molecules and its molecular fragments by MD simulation. These FF parameters are obtained from 'frcmod.parm' files internally stored in the PyRED program, and in the 'frcmod.user' file, that can be provided as an input file in the archive file.
• By default bond and angle FF constants are rounded off at +/- 5 kcal.mol^-1.ang^-2 and kcal.mol^-1.rad^-2, respectively: we do beleive, that using more accurate values is meaningless (see the 'FFPARM_ROUND' keyword in the 'System.config' file).
• Generic dihedral angle FF parameters are replaced by specific ones by providing the terminal atom types and by dividing the potential value in kcal.mol^-2.rad^-1 by the number of paths.

    -2- The frcmod.correspondence file

• The 'frcmod.correspondence' file reports FF parameters determined by analogy to known ones using an internal algorithm implemented in PyRED: the latter has to be developed.

    -3- The frcmod.unknown file

• The 'frcmod.unknown' file lists the missing FF parameters needed to study the PyRED input molecules and its molecular fragments by MD simulation. These missing FF parameters can be provided in the 'frcmod.user' input file in a new PyRED job.
• How to generate missing FF parameters?
  • Missing van der Waals parameters
    • The required van der Waals parameters may be obatained by using a google search; for instance using the following keywords: 'chemical element' molecular dynamics AMBER force field.
  • Missing bond and angle equilibrium values
    • Measure the needed equilibrium value from the X-ray structure of a small molecule (see the Cambridge Structural Database), or
    • Measure the needed equilibrium value from geometry optimization using a high theory level in quantum chemistry (QM) such as B3LYP/cc-pVTZ or WB97XD/cc-pVTZ.
  • Missing bond and angle constant values
    • Simply determine the needed constant value by analogy to an existing one involving similar atom types (indeed the bond and angle FF constant values are not of a primary importance for computing an accurate geometry; FF constants are more important to reproduce QM frequencies).
  • Missing improper dihedral angle parameters
    • Improper dihedral angle parameters are not mandatory; the LEaP program accepts missing improper dihedral angle parameters.
    • An improper dihedral angle parameter can also be determined by analogy to an existing one involving similar atom types.
    • The potential of an improper dihedral angle parameter can also be set to zero.
  • Missing dihedral angle parameters
    • Determine the dihedral angle parameters (potential, phase and number of paths) by analogy to an existing one involving similar atom types. However, particular attention has to be paid to these parameters as they are crucial to define an accurate geometry!
    • Key dihedral angle parameters have to be accuratly computed by fitting the entire dihedral deformation profile versus high theory level QM computations.

    -4- The LEaP script

• The 'LEaP script' allows loading FF libraries and FF parameters files generated by PyRED in the LEaP program to generate the topological 'prmtop' and the coordinate 'prmcrd' files usefull to initiate MD simulation.