
               -----------------------------------------------
               PARAMS Directory for the TINKER Program Package
               -----------------------------------------------

      This directory contains the force field parameter sets distributed
      with the TINKER package, implementing a selection of widely-used
      literature force fields as well as the AMOEBA force field now
      under development in the Ponder lab. We try to exactly reproduce
      the intent of the original authors of our distributed, third-party
      force fields. In all cases the parameter sets have been validated
      against literature reports, results as provided by the original
      developers, or calculations made with the authentic programs. With
      the few exceptions noted below, TINKER calculations can be treated
      as authentic results from the genuine force fields. Please inform
      the TINKER developers of any discrepancies. A brief description of
      each parameter set is provided below:

      amber94    AMBER ff94 parameters for proteins and nucleic acids.
                 Note that N- and C-terminal amino acid charges differ
                 slightly from the authentic charge values. For these
                 terminal residues some charge is redistributed to or
                 from the alpha carbon atom; the total magnitude of the
                 redistribution is less than 0.01 e- in most cases. The
                 file reproduces the authentic ff94 energies.

      amber96    AMBER ff96 parameters for proteins and nucleic acids.
                 The only changes from AMBER ff94 are in the phi/psi
                 torsional parameters.

      amber98    AMBER ff98 parameters for proteins and nucleic acids.
                 The only changes from AMBER ff94 are in the glycosidic
                 torsional parameters.

      amber99    AMBER ff99 parameters for proteins and nucleic acids.
                 Uses the Cornell, et al (parm94) electrostatic model
                 but changes several geometric values from the above
                 Amber force fields.

      amoeba     AMOEBA force field for various small molecules based
                 on polarizable atomic multipole electrostatics.

      amoebapro  Protein parameters for the AMOEBA polarizable atomic
                 multipole force field.

      charmm19   CHARMM19 parameters for proteins and water. The nucleic
                 acid values are not yet implemented. There are some
                 differences between authentic CHARMM19 and the TINKER
                 version due to replacement of CHARMM impropers by
                 torsions for cases that involve atoms not bonded to
                 the trigonal atom and TINKER's use of all possible
                 torsions across a bond instead of a single torsion
                 per bond. 

      charmm27   CHARMM27 parameters for proteins, heme and some lipids.
                 Most of the nucleic acid and small model compound values
                 are not yet implemented. The file is almost exactly
                 reproduces authentic CHARMM energies; the differences
                 are related to TINKER symmetrizing some impropers.

      dang       Polarizable force field parameters from Liem Dang at
                 Pacific Northwest National Laboratory.

      dudek      Scaled HF/6-31G* atomic multipole parameters from a
                 preliminary force field by Dudek and Ponder. The file
                 contains all the multipole values from the 1995 JCC
                 paper. These values are now obsolete, and are largely
                 superceeded by the polarizable AMOEBA force field.

      encad      ENCAD parameters for proteins and nucleic acids
                 (in preparation).

      hoch       Simple NMR-NOE force field of Hoch and Stern.

      merck      MMFF94 van der Waals parameters as taken from the
                 1992 Halgren JACS paper on the Buffered 14-7 potential.

      mm2        Full MM2(1991) parameters including pi-systems. The
                 anomeric and electronegativity correction terms are
                 not implemented.

      mm3        Full MM3(2000) parameters including pi-systems. The
                 directional hydrogen bonding and electronegativity
                 bond length correction terms are implemented, but
                 the anomeric and Bohlmann correction terms are not
                 implemented.

      mm3pro     Protein-only version of the MM3 parameters. The
                 dielectric constant and some bond stretch and torsion
                 parameters are set to values recommended for high
                 dielectric and/or bulk environments.

      oplsaa     OPLS-AA with all-atom parameters for proteins and many
                 general classes of organic molecules.

      oplsaal    An updated version of OPLS-AA with modified torsional
                 parameters for the protein backbone and side chains.

      oplsua     Complete OPLS-UA with united-atom parameters for proteins
                 and many classes of organic molecules. Explicit hydrogens
                 on polar atoms and aromatic carbons.

      smooth     Parameters for use with the TINKER potential energy
                 smoothing methods. Largely adapted largely from
                 OPLS-UA with modifications to the vdw and improper
                 torsion terms.

      smoothaa   Similar to SMOOTH, but based on OPLS-AA parameters.

      water      The current AMOEBA water parameters for a polarizable
                 multipole electrostatics model. This model is equal to
                 or better than the best available water models for many
                 bulk and cluster properties.

