Force Field Modifications

Rather than regarding the force field as a fixed part of the refinement procedure, it may be quite reasonable to adjust force field parameters to make barriers easier to surmount or to use force field parameters as variables that can be altered to implement a refinement method. In one sense, this principle of minimizing on a changing potential surface could be seen as the heart of the variable target function method discussed previously.8 

In the case of MD, this principle is best shown by the force field that has often been used by Clore, Gronenborn, and co-workers.89 ,04 105 The non-bonded terms were replaced by a simple repulsive potential Vrepe of the form 

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From the results described above, MD on DNA has progressed considerably since the early 1980s, a number of features of both DNA structure and environmental effects are well described by simulation, and recently proposed force field modifications show improved if not fully satisfactory behavior. The CHARMM Parm.23 force field shows a marked unnatural preference for A form structures and thus inferences about the structure and dynamics of B form DNA are unreliable. The incipient tendency in the AMBER Cornell et al. force field to preferentially stabilize B form structures which originally could not be excluded has proven in subsequent studies to be real. Thus B-DNA dynamics may be reasonably well described, but an unnatural reluctance of AMBER MD to... 

Time-reversible energy conserving methods can be obtained by appropriate modifications to the (time-reversible) midpoint method. Two such modifications are (i) scaling of the force field by a scalar such that total energy... 

UFF is the most reliable force field to be used without modification for inorganic systems. 

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. 

The force fields available are MM2, MM3, AMBER, OPLSA, AMBER94, and MMFF. The asterisk ( ) indicates force fields that use a modification of the original description in the literature. There is support for user-defined metal atoms, but not many metals are predefined. MM2 has atom types for describing transition structures. The user can designate a substructure for energy computation. 

More recently, Ponder and co-workers [40-48] developed the AMOEBA force field based on a modification of the formulation of Applequist [49] and Thole [50], It is based on a modification of Eq. (9-3) with the static electric field due to permanent charges replaced by permanent multipoles ... 

The next two steps in the procedure of Leonard and Ashman are the conversion of the diagonal elements from atomic units into force field units and calculation of scaling factors for bond lengths and angles. The calculated force constants had to be scaled down by approximately 25% and 70% to yield force constants comparable in numerical size with those included in MM2. Neither force constants nor scaling factors can be incorporated directly into a different force field. A modification of the described procedure that meets the requirements of CVFF was developed. Fragments with known force field parameters were chosen. After a full geometry optimization (HF/6-31G ) second derivatives and vibrational frequencies were calculated. The force... 

For these vibrations, the quantization scheme of Section 4.2 can be carried over without any modification (Iachello and Oss, 1991a). The potentials in each stretching coordinate 5 are in an anharmonic force field approximation represented by Morse potentials. The boson operators (Ot,xt) correspond to the quantization of anharmonic Morse oscillators, with classical Hamiltonian... 

Several modifications of the Engler-Schleyer force field have appeared. White (27) added olefin parameters and used an efficient two-stage Newton-Raphson minimization modification. The accuracy of the White force field regarding heat of formation calculations is... 

Various hybridization states of the phosphorus atom have been parameterized in various force fields (Table 9). If a force field is to be useful for pentacoordinated phosphoranes, the relative energies of the two basic configurations, trigonal bypyramid (62) and square pyramid (63), must be differentiated. For this purpose, a 1,3-non-bonded interaction term centered only at the central phosphorus atom was added to MMI. In this modification, account was ts en of... 

Modification of the AMBER Force Field for Simulations on Complex Carbohydrates... 

The magnitude of friction can be appreciably reduced if boundary lubrication decreases the force field. This may be achieved by adsorbed films (Figure 5.12). However, one may expect that this is a highly idealized model, and some modifications will be necessary. 

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