The database directory.

There are two main types of force field file in the amber6/dat/ directory: residue descriptions for building the topolgy database, and force field files. The residue descriptions include topologies, atom types and charges and have .in extensions. The PARM force field files contains parameters mapped to the atom types: mass, Van der Waals, bond, angle, torsional and hydrogen bonding terms. These files have names matching the pattern, parm*.dat.

The following files are found in the database directory amber6/dat/:

Amber 1994 (Cornell et al.) force field
all_nuc94.in Nucleic acid input for building database.
all_amino94.in Amino acid input for building database.
all_aminoct94.in COO- amino acid input for database.
all_aminont94.in NH3+ amino acid input for database.
nacl.in Ion file
parm94.dat 1994 force field file.
parm96.dat modified version of 1994 force field, for proteins
parm98.dat modified version of 1994 force field, for nucleic acids



Amber 1984, 1986 (Weiner et al.) force fields
all.in All atom database input.
allct.in All atom database input, COO- Amino acids.
allnt.in All atom database input, NH3+ Amino acids.
uni.in United atom database input.
unict.in United atom database input, COO- Amino acids.
unint.in United atom database input, NH3+ Amino acids.
parm91.dat Parameters for 1984, 1986 force fields



OPLS-related files:
opls_uni.in Normal OPLS residues.
opls_unict.in OPLS COO- Amino acids.
opls_unint.in OPLS NH3+ Amino acids.
opls_parm.dat OPLS force field file.



Miscellaneous:
wat216.dat Cube of 216 TIP4P waters, MC liquid.
nucgen.dat Nucgen nucleic acid conformations.
PROTON_INFO* Files needed for protonate

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1994 parameters. These are parameters from W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, "A second generation force field for the simulation of proteins, nucleic acids, and organic molecules". J. Am. Chem. Soc. 117, 5179-5197 (1995). These parameters are especially derived for solvated systems, and when used with an appropriate 1-4 electrostatic scale factor, have been shown to perform well at modelling many organic molecules. The parameters in parm94.dat omit the hydrogen bonding terms of earlier force fields. This is an all-atom force field; no united-atom counterpart is provided. 1-4 electrostatic interactions are scaled by 1.2 instead of 2.0; users must make this adjustment in their input files for sander, gibbs etc. when using this force field.

Charges were derived using the 6-31G* basis set, because this exaggerates the dipole moment of most residues by 10-20%. It thus "builds in" the amount of polarization which would be expected in aqueous solution. This is necessary for carrying out condensed phase simulations with an effective two-body force field which does not include explicit polarization. The charge-fitting procedure is described at length in the Appendix.

parm96.dat differs from parm94.dat in that the torsions for phi and psi have been modified in response to ab initio calculations performed by Beachy et al. [J. Am. Chem. Soc. 119, 5908-5920 (1997)], which showed that the energy difference between conformations were quite different than calculated by Cornell et al. (using parm94.dat). To create parm96.dat, common V1 and V2 parameters were used for phi and psi, which were empirically adjusted to reproduce the energy difference between extended and constrained alpha helical energies for the alanine tetrapeptide. This led to a significant improvement between molecular mechanical and quantum mechanical relative energies for the remaining members of the set of tetrapeptides studied by Beacy et al. This model (parm96.dat) is described by in P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot and A. Pohorille, "The development/application of a 'minimalist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data." In Computer Simulation of Biomolecular Systems, Vol. 3 A. Wilkinson, P. Weiner, W. Van Gunsteren, eds. (Elsevier, 1997), pp. 83-96.

parm98.dat differs from parm94.dat in torsion angle parameters involving the glycosidic torsion in nucleic acids. These serve to improve the predicted helical repeat and sugar pucker profiles. The changes are described in T.E. Cheatham, III, P. Cieplak and P.A. Kollman, "A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat." J. Biomol. Struct. Dyn. 16, 845-861 (1999).

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1984, 1986 parameters. These parameters sets are described in two papers: (a) S.J. Weiner, P.A. Kollman, D.A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr., and P. Weiner, "A new force field for molecular mechanical simulation of nucleic acids and proteins". J. Am. Chem. Soc. 106, 765-784 (1984). and (b) S.J. Weiner, P.A. Kollman, D.T. Nguyen, and D.A. Case, "An all-atom force field for simulations of proteins and nucleic acids". J. Computat. Chem. 7, 230-252 (1986). These parameters may still be useful for vacuum simulations of nucleic acids and proteins using a distance-dependent dielectric. The material in parm91.dat is the parameter set distributed with Amber 4.0. The STUB nonbonded set has been copied from parmuni.dat; these sets of parameters are appropriate for united atom calculations using the "larger" carbon radii referred to in the "note added in proof" of the 1984 JACS paper. If these values are used for a united atom calculation, the parameter scnb should be set to 8.0, not its default value of 2.0.

A number of terms in the non-bonded list of parm91.dat should be noted. The non-bonded terms for I(iodine),CU(copper) and MG(magnesium) have not been carefully calibrated, but are given as approximate values. In the STUB set of non-bonded parameters, we have included parameters for a large hydrated monovalent cation (IP) that represent work by Singh et al 1985 on large hydrated counterions for DNA. Similar values are included for a hydrated anion (IM).

For alkali ions with explicit waters, we have provided the values of Åqvist (J. Phys. Chem., 1990, 94: 8021-8024) which are adjusted for Amber's nonbonded atom pair combining rules to give the same ion-OW potentials, in order to reproduce the first peak of the radial distribution for ion-OW and the relative free energies of solvation in water of the various ions. These are included in the standard (STDA) parameter file. The atom types are:

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OPLS. The file opls_parm.dat is a parameter set appropriate for use with the AMBER/OPLS parameter set as described by Tirado-Rives and Jorgensen: W.L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc. 1988, 110, 1657.

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