Quanta/CHARMm

AMBER, GROMOS, QUANTA/CHARMm molecular dynamics (see text)... 

Figure 5 Conformers of the N-terminal decapeptide TTLTEPEPDL from the leech protease hementin. Molecular modeling predictions using Quanta/CharmM of two low-energy conformers.131...

PCMODEL are supported by developers at Columbia University and Indiana University, respectively. Neither is backed by a large marketing or sales force. Yet each has enjoyed noteworthy success in terms of being used in publications. Also plotted are CJACS hits of Chemical Design Ltd., which supports Chem-X, and Serena Software, which has PCMODEL. Literature mention of the Chem-X package exceeded that of Insight/Discover, SYBYL, and Quanta/CHARMm for at least one year in the 1980s, but publications from users of Chem-X have not kept up and have fluctuated around the same level in the last few years. 

Molecular mechanics minimization and molecular dynamics were chosen to examine the possible conformations for the two acyl enzymes and conclusions were drawn from the time evolution of the two systems. The starting point was a crystal structure of phenylethaneboronic acid bound to alpha-chymotrypsin. QUANTA/CHARMM (Brooks et al, 1983) was employed for the calculations. Ninety-five water molecules from the X-ray structure were included. Distance monitoring and the creation ofH-bonds were the main criteria for differentiating between the two molecules. Both acyl enzymes have their ketone carbonyls H-bonded to Gly-216 NH. Both start with their ester carbonyl in the oxyanion hole (H-bonded to Ser-195 and to Gly-193). The R-acyl enzyme looses both of these hydrogen bonds during the simulation. Attack of water on the R-species should, thus, be less frequently successful. Values for differences in energy were not used because of a small... 

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Quanta/CHARMm, Molecular Simulations, Warmshurst, Mass., U.S.A. 

Scheme 7. The stractures of the rccc isomer with substituents R at the bottom (QUANTA /CHARMm simulation for R = C7H15).

Scheme 10. QUANTA/CHARMm simulation of the complex 3 + Me3N-(CH2)ioNMe3 and complexation free energies [ kJ/mol] of 3 with substrates of different chainlength. Complexa-tion induced NMR shifts (all upheld CIS, in [ppm]) are in italics.

Force field parametrization Energy minimization methods Software introduction (QUANTA CHARMM)... 

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