
               -----------------------------------------------
               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.

      amber99sb  Amber ff99sb parameters for proteins and nucleic acids.
                 The only changes from Amber ff99 are to torsional
                 parameters for phi/psi and phi'/psi' (angles to the
                 beta carbon atom).

      amoeba     AMOEBA force field for various small organic molecules
                 based on polarizable atomic multipole electrostatics.
                 Both 2004 (amoeba04) and 2009 (amoeba09) are provided.

      amoebabio  Biopolymer parameters (protein and nucleic acid) for
                 the AMOEBA polarizable atomic multipole force field.
                 The 2009 version is provided.

      amoebapro  Protein parameters for the AMOEBA polarizable atomic
                 multipole force field. The original 2004 version is
                 provided.

      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. 

      charmm22   CHARMM22 parameters for proteins, plus heme and lipids.
                 Most of the nucleic acid and small model compound values
                 are not yet implemented. The file almost exactly
                 reproduces authentic CHARMM energies; there are small
                 differences are related to TINKER symmetrization of some
                 improper torsions.

      charmm22   CHARMM22 parameters for proteins, plus heme and lipids.
        -cmap    Contains the CMAP torsion-torsion phi-psi correction.
                 Most of the nucleic acid and small model compound values
                 are not yet implemented. The file almost exactly
                 reproduces authentic CHARMM energies; there are small
                 differences are related to TINKER symmetrization of some
                 improper torsions, as well as in the CMAP correction.

      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.

      iwater     The current AMOEBA water parameters for a polarizable
                 multipole model including only "direct" (non-iterative)
                 polarization. The parameters were fit to a variety of
                 water properties using the Force Balance method of
                 Lee-Ping Wang.


      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.

      mmff       Full MMFF94 parameters for the Merck Molecular Force
                 Field. Validated against the data suite deposited with
                 the Computational Chemistry List (CCL)

      oplsaa     OPLS-AA from July 2008 with all-atom parameters for
                 proteins, nucleic acids and many general classes of
                 organic molecules.

      oplsaal    An modified version of 1997 OPLS-AA with optimized
                 torsional parameters for the protein backbone and side
                 chains as published in 2001.

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

      smoothaa   Parameters for use with the TINKER potential energy
                 smoothing methods. Based on the OPLS-AA parameters, but
                 with modifications to vdw and improper torsion terms.

      smoothua   Similar to SMOOTHAA, but based on OPLS-UA parameters.

      tiny       A generic parameter file intended to enable simple
                 geometry optimization of crude structures to avoid
                 steric clashes. The bond, angle and torsion parameters
                 are set to idealized values. The vdw values are loosely
                 based on OPLS. Electrostatics is neglected completely.

      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.

