CHARMM Element doc/cff.doc 1.1^_File: CFF, Node: Top, Up: (chmdoc/commands.doc), Next: Usage Consistent Force Field (CFF)* Menu:* Usage:: How to use CFF with CHARMM standalone* Status:: Current status of CFF implementation in CHARMM* Theory:: Basis for, parameterization and performance of CFF* Funcform:: Functional form of the CFF energy expression* Refs:: References to papers describing CFF^_File: CFF, Node: Usage, Up: Top, Next: Status, Previous: TopIn order to use CFF in CHARMM, the user has to issue the followingcommands:1. use cff2. read cff parameter file3. (a) read rtf name <CFF-capable rtf file>, or (b) read psf name <file_name>4. read sequence ! if input is via the rtf route (step 3 (a))5. generate6. read coord, or ic build ! if input is via the read rtf/sequence route.When using CFF95 or later Step 3a requires a CFF-capable rtf file. This meansa file in which BOND records have been replaced by analogous DOUBLE records forcases in which the chemical structure has a double bond. Note that CFF-capablertf files are *back compatible*. That is, such rtf files can equally well beused for calculations that utilize the CHARMM force field. Thus, it is *not*necessary to maintain two versions of the rtf files.NOTE: 1. no binary parameter files are supported for CFF. 2. CFF is an all hydrogen force field -- i.e., extended atoms are not supportedExamples of CFF usage in CHARMM are given in the ccfftest directory.^_File: CFF, Node: Status, Up: Top, Next: Theory, Previous: UsageStatus of CFF implementation into CHARMM (May 2001)=============================================================This implementation of CFF in CHARMM is principally due to RickLapp (MSI) and William Young (MSI).Features currently supported in CHARMM/CFF (1) energy and first derivatives (2) minimization (3) dynamics (4) most ATOM based cutoff optionsMajor features NOT currently implemented in CHARMM/CFF: (1) bonds between primary atoms and image atoms. (2) Cutoff options currently not supported are group-based cutoffs, distance shifting and force-based switching. (3) Fast multipoles.Other known limitations: (1) correlation analysis tools have not been implemented for CFF specific energy terms -- e.g. it is not possible to calculate the correlation function for an out-of-plane bending angle, etc ... (2) only all-atom models (no extended atoms)There are probably other problems/limitations/bugs. Your comments aboutlimitations of the current CFF implementation in CHARMM (and bugs) will bevery valuable.Please direct comments to:William Young, MSIe-mail: [email protected]: (619)799-5348KNOWN BUGS:^_File: CFF, Node: Theory, Up: Top, Next: Refs, Previous: StatusThe aim of the CFF development is a force field that is: * broad, covering a relatively large number of differing functional groups, * accurate, achieved via accurate reproduction of the quantum mechanical energy surfaces, * consistent between differing phases and molecular environments, * applicable to a wide range of molecular properties, * consistent between differing types of molecules, such as interaction of protein active sites with ligands, or assemblies of proteins with nucleic acids or with solvent.Quantum mechanical forcefieldsThe intramolecular parameters constituting the current generation offorcefields are based on the energies and energy derivatives computed byab initio quantum mechanical procedures for a series of model compounds.CFF uses quantum computations in the Hartree-Fock approximation with the6-31G* basis set to expand the wavefunctions [1][2]. The quantummechanical energies and the energy first derivatives (gradients) andsecond derivatives (Hessians) were computed for the equilibrium molecularstructures, at conformational energy barriers, and for a set of distortedstructures. The distorted molecular structures were generated by randomlydeforming all the internal coordinates, as well as by systematicallyrotating about individual bonds. These quantum observables were fit tothe energy expression to obtain the Class II parameters [3][4]. Many ofthe atomic partial charges were also determined quantum mechanically.The intermolecular parameters of the forcefield may also, in principle,be computed quantum mechanically [5]. The remaining CFF forcefieldintermolecular or nonbond parameters were computed by fitting toexperimental crystal lattice constants and sublimation energies ofcrystals [6][7][8].Internal energy termsThe energy of the molecule or assembly is expressed in terms of internalcoordinates such as bond lengths, bond angles, and dihedral angles. ForClass II forcefields this set of descriptors is greatly expanded byincluding cross terms, that is, the interactions between bondlengths and angles, between pairs of angles, etc. CFF contains, in all,twelve types of energy terms: bond stretching, valence angle bending,valence dihedral angles, out-of-plane deformation, and eight cross terms.The cross terms extend the accuracy and range of application of theforcefield by including the effect of neighboring atomic positions oneach of the bond lengths, valence angles, and dihedral angles.^_File: MMFF, Node: Funcform, Up: Top, Next: Refs, Previous: TheoryEnergy functional formsThe energy expression may be decomposed into diagonal terms that dependon a single molecular internal coordinate such as a bond length, couplingterms between internal coordinates, and nonbond internuclear distances.This energy is fit to the quantum mechanical energy.1. Bond stretching.Ebond = K2 * (b - b0)^2 + K3 * (b - b0)^3 + K4 * (b - b0)^4 (1)where K2, K3 and K4 are the quadratic, cubic and quartic forcefieldparameters or force constants, b is the bond length, and b0 is thereference value of the bond length.2. Angle bending.Eangle = K2 * Delta^2 + K3 * Delta^3 + K4 * Delta^4 (2)where Delta = Theta - Theta0 is the difference between the actual andreference bond angles.3. Out-of-plane bending.Eoop = K * (Chi - Chi0)^2 (3)where chi is an out-of-plane coordinate as defined by Wilson et al.[9]4. Torsion energy, in order to reflect differing hybridizations aboutthe bonded atoms, must contain one-, two-, and threefold periodic terms:Etorsion = SUM(n=1,3) { V(n) * [ 1 - cos(n*Phi - Phi0(n)) ] } (4)where phi is a dihedral