CHARMM

Bernhard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. CHARMM A program for macro-molecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4(2) 187-217, 1983. 

The solvent dielectric constant, ionic strength and temperature are chosen to fit the conditions of the experimental studies. The protein dielectric constant is assigned some small value, e.g. 4. The PB calculations are currently carried out with the atomic charges and radii of the PARSE parameter set, developed by Honig and coworkers [17] or that for CHARMM [12]. The PARSE parameter set... 

Very recently, we have developed and incorporated into the CHARMM molecular mechanics program a version of LN that uses direct-force evaluation, rather than linearization, for the fast-force components [91]. The scheme can be used in combination with SHAKE (e.g., for freezing bond lengths) and with periodic boundary conditions. Results for solvated protein and nucleic-... 

P. Derreumaux, G. Zhang, B. Brooks, and T. Schlick. A truncated-Newton method adapted for CHARMM and biomolecular applications. J. Comp. Chem., 15 532-552, 1994. 

Watanabe, M., Karplus, M. Dynamics of Molecules with Internal Degrees of Freedom by Multiple Time-Step Methods. J. Chem. Phys. 99 (1995) 8063-8074 Figueirido, F., Levy, R. M., Zhou, R., Berne, B. J. Large Scale Simulation of Macromolecules in Solution Combining the Periodic Fast Multiple Method with Multiple Time Step Integrators. J. Chem. Phys. 106 (1997) 9835-9849 Derreumaux, P., Zhang, G., Schlick, T, Brooks, B.R. A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. J. Comp. Chem. 15 (1994) 532-555... 

In this case, only two parameters (k and Iq) per atom pair are needed, and the computation of a quadratic function is less expensive. Therefore, this type of expression is used especially by biomolecular force fields (AMBER, CHARMM, GROMOS) dealing with large molecules like proteins, lipids, or DNA. 

N is the number of point charges within the molecule and Sq is the dielectric permittivity of the vacuum. This form is used especially in force fields like AMBER and CHARMM for proteins. As already mentioned, Coulombic 1,4-non-bonded interactions interfere with 1,4-torsional potentials and are therefore scaled (e.g., by 1 1.2 in AMBER). Please be aware that Coulombic interactions, unlike the bonded contributions to the PEF presented above, are not limited to a single molecule. If the system under consideration contains more than one molecule (like a peptide in a box of water), non-bonded interactions have to be calculated between the molecules, too. This principle also holds for the non-bonded van der Waals interactions, which are discussed in Section 7.2.3.6. 

Th c fun ction al form for bon d stretch in g in HlOa, as in CHARMM, is quadratic only and is identical to that shown in equation (1 1) on page I 75. Th e bond stretch in g force con stan ts are in units of... 

Chemistry at Harvard macromolecular mechanics (CHARMM) is the name of both a force field and a program incorporating that force field. The academic version of this program is designated CHARMM and the commercial version is called CHARMm. It was originally devised for proteins and nucleic acids. It has... 

The AMBER and CHARMM force fields are best suited for protein and nucleic acid studies. 

ChemSketch has some special-purpose building functions. The peptide builder creates a line structure from the protein sequence defined with the typical three-letter abbreviations. The carbohydrate builder creates a structure from a text string description of the molecule. The nucleic acid builder creates a structure from the typical one-letter abbreviations. There is a function to clean up the shape of the structure (i.e., make bond lengths equivalent). There is also a three-dimensional optimization routine, which uses a proprietary modification of the CHARMM force field. It is possible to set the molecule line drawing mode to obey the conventions of several different publishers. 

CHARMM (chemistry at Harvard macromolecular mechanics) a molecular mechanics force field... 

Note The BIO+ force field is an implementation of the CHARMM (Chemistry at HARvard Macromolecular Mechanics) force field developed in the group of Martin Karplus at Harvard University. Like AMBER and OPLS, it is primarily designed to explore macromolecules. 

Brooks, B.R. Bruccoleri, R.E. Olafson, B.D. States, D.J. Swaminathan, S. Karpins, M. CHARMM A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 187-217, 1983. 

The first modification is to simply scale the dielectric permittivity of free space (8 ) by a scale factor D to mediate or dampen the long range electrostatic interactions. Its value was often set to be between 1.0 and 78.0, the macroscopic value for water. A value of D=2.5, so that 8 =2.58q, was often used in early CHARMM calculations. 

The HyperChem BIOh- force field gives results equivalent to CHARMM using the same CHARMM parameter sets. 

HyperChem uses the improper dihedral angle formed by central atom - neighbor 1 - neighbor 2 - neighbor 3, where the order of neighbors is how they appear in a HIN file. Not all planar atoms customarily have associated improper torsions. The order of atoms is arbitrary but has been consistently chosen by the original authors of the CHARMM force field. The templates contain equivalent CHARMM definitions of improper torsions for amino acids. Improper dihedral angles cannot be defined that do not have a central atom, as is sometimes done in CHARMM calculations. 

The 1-4 van der Waals interactions cannot be scaled in CHARMM but in newer CHARMM parameter sets some atom types (usually united atoms) use different parameters for 1 interactions. These are specified for BlO-t in the file pointed to by the 6-12Atom 14VDW entry, usually called nbd.txt(dbf). If an atom type is absent in the 6-12Atom 14VDW file, the normal parameters are used. The format of the 6-12Atom 14VDW file is also specified by the 6-12AtomVDWFormat entry for the parameter set. 

Newer, published CHARMM parameter sets override some of the combination rule generated parameters for some atom type pairs. These parameters are found in the file pointed to by the 6-12PairVDW entry for the parameter set, usually called npr.txt(dbf). The values of Ay and By for these are computed using equations (22) and (23) on page 178 by setting the 6-12PairVDWFormat entry to RStarEpsilon. 

The BIOh- force field option in HyperChem has no hydrogen bonding term. This is consistent with evolution and common use of the CHARMM force field (even the 1983 paper did not use a hydrogen bonding term in its example calculations and mentioned that the functional form used then was unsatisfactory and under review). 

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