####################################### PARAMS Directory for the Tinker 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 and 2018 versions are provided. amoebanuc Nucleic acid parameter for the AMOEBA polarizable atomic multipole force field. The 2017 version is provided. amoebapro Protein parameters for the AMOEBA polarizable atomic multipole force field. The original 2004 version and current 2013 version are provided. basic 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 largely neglected. 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). hippo Preliminary parameters from 2018 for the HIPPO model covering the monomer molecules in the S101 database. 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 using the Force Balance method. 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. water03 The original 2003 AMOEBA water model parameters for a polarizable multipole electrostatics model. water14 Parameters for a revision of the 2003 AMOEBA water model fit to cluster data and a number of liquid properties using the Force Balance optimization method. water19 Initial unpublished parameters for a HIPPO water model fit to clusters, liquid properties and ice without and charge flux terms. water21 Final HIPPO water parameters including charge flux terms.