Cornell et al. force field

In the majority of continuum solvation models incorporating a surface-tension approach to estimating the non-electrostatic solvation components, the index k in Eq. (11.22) runs over a list of atom types, and die user assigns the appropriate type to each atom of the solute. This is particularly straightforward for MM models, like the Generalized Bom/Surface Area (GB/SA) model (Still el al. 1990 see also Best, Merz, and Reynolds 1997), since atom types are already intrinsic to the force field approach. This same formalism has been combined with the CHARMM and Cornell et al. force fields (see Table 2.1) to define GB models for proteins and nucleic acids (Dominy and Brooks 1999 Jayaram, Sprous, and Beveridge 1998). Considering this approach applied within the QM arena, the MST-ST models of Orozco and Luque have been the most extensively developed (see, for instance, Curutchet, Orozco, and Luque 2001). 

Cheatham TE, III, P Cieplak, PA Kollman (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16 (4) 845-862... 

Stacked NA base pairs AMBER 4.1 with the force field of Cornell et al [16] best reproduces the ab initio stabilization energies and geometries. The success of the Cornell et al force field is probably due to the derivation of atomic charges. It must be also mentioned that this force field provides a better description of interaction energies of NA base pairs than any semiempirical quantum chemical method or even nonempirical ab initio technique of a lower quality than that of the MP2 procedure (DFT or ab initio HF methods). 

Simulations were performed with the NAMD simulation package (version 2.6) [83] using the all-atom Cornell et al. force field (parm99) [84], generated with the AMBER 10 package [85-87] and TIP3P water model [88]. Periodic boundary... 

All models were generated with the TLEAP module of the AMBER 4.1 program suite (41) with the Cornell et al. force field (48), using fat sodium ions for the neutralization of the phosphate charges. The 5 -end was modeled without the triphosphate group which is present in the real sample. All structural analysis was carried out with the CARNAL module. 

Thus, dynamical models of oligonucletide sequences based on the Cornell et al. force field and AMBER 4.1 MD give a reasonable account at the molecular level of many of the salient features observed for the sequence dependent helix morphology of sequences with A-tracts phased by a full helical turn. A series of... 

Simulations of an RNA hairpin loop showed that its structure was tremendously stable on a nanosecond time scale (13) and simulations of a RNA duplex showed that in addition to A-RNA, B-RNA is also stable on a nanosecond time scale (31). This brings up the issue of conformational sampling in simulations of RNA with the Cornell et al. force field which has been extensively studied in our lab. At the meeting, we presented the results of five unrestrained molecular dynamics simulations of an RNA tetraloop, describing our efforts to observe the conversion between an... 

In this context, we would like to emphasize the often blurred distinction between force field , the functional form and parameters, and the computer program used. The force field used by Weiner et al. (often called the AMBER force field ) has been implemented within the TRIPOS, DISCOVER, and MACROMODEL programs. In principle, the Cornell et al. force field, because of its simple functional form, could be implemented within all the programs mentioned above, with only minor modifications required in a few cases. On the other hand, for example, AMBER could not, without major changes, implement the MM4 force field. In our opinion, force field parameters, in contrast to the software in which they are used, must be made available in their entirety when an article using them is published, either in the article or an appendix or through the World Wide Web. A publication is not really science unless its results can be reproduced by others ... 

Sprous et al. have studied the A/B conformational preferences of d(CGCGAATTCGCG) in water and 85% ethanol and other mixed solvent systems using AMBER 4.1 MD and the Cornell et al. force field with PME boundary conditions. The question addressed is simply characterization whether... 

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... 

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