CHARMM program

To illustrate the different complexities, CHARMM s energies arising from torsional terms depend only on the two central atoms, and there is only one cosine term. For MM2 and MM3, there are three cosine terms for each four-atom sequence that defines a torsion angle. MM2 treats lone pairs of electrons on hydroxyl and ether oxygen atoms as separate "atoms that also must be parameterized. Therefore, many more parameters must be used with the MM2 and MM3 programs than the CHARMM program. (The parameters for all the atomic sequences in glucose, and many other molecules, are furnished with MM2 and MM3.)... 

We thank J. Apostolakis and Professor A. Pluckthun for helpful discussions. The calculations were performed on an SGI Indigo2 and an eight-processor SGI Challenge (R4400 processors). The CHARMM program within the version 4.0 of the QUANTA software package (Biosym-MSI Inc) was used for some of the minimization performed in this work. The CCLD program is available from A. Caflisch. 

Molecular mechanics calculations with the CHARMm program of the DAB-tfen[Pg.59]

Leusen et al. studied the crystal packing of ephedrine with several phosphoric acid stereoisomers to verify whether a relationship between enthalpy of formation and separation of enantiomers via diastereomeric salt formation exists.They considered four different force fields and determined that the CHARMM program, as implemented in QUANTA, was the best for their application. Their decision was based mainly on the knowledge that non-bonded cutoff distances are larger in CHARMM. A larger cutoff distance is necessary to account for the interaction between different hydrophobic layers in the crystal (interlayer distances of 14—16 A). These authors were unable to quantitatively determine the validity of their hypothesis, although qualitative explanations were derived for their observations. 

Molecular mechanics calculations on the calix[4]arenetetrathiol 95k using the CHARMm program indicates the stability sequence to be 1,3-alternate > partial cone > 1,2-alternate > cone. 

One should distinguish between a force field, which is defined by the expression for V in (16.94), and a molecular-mechanics program, which is a computer program that uses a force field to perform molecular-mechanics calculations. Sometimes MM programs and force fields have the same name. For example, CHARMM is also the name of a molecular-mechanics program. The CHARMM program has available in it, not only the CHARMM force field, but also MMFF94. 

To explore the possible solution conformers, Guo et al. [82] performed QM/MM molecular dynamics simulations using the CHARMM program [86] the CHAIR... 

A harmonic dynamic analysis of the BPTI using the CHARMM program potential function has recently been performed in the full conformational space of the molecule [28] that is, all bond lengths and angles, as well as dihedral angles, are included for the 580 atom system consisting of all heavy atoms and polar hydrogens. 

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