CHARMm library

Tel. 800-424-9737, fax 415-491-8311 (U.S.A.), tel. 41-38-337633 (U.K.) Model building, display, charge density, electrostatic potential, and molecular orbital plots. Stick, sphere, and dot surface display. 2D to 3D conversion. Protein and DNA fragment libraries. MM+, BIO+ (implementations of MM2 and CHARMM, respectively), OPLS, and AMBER molecular mechanics and dynamics. Solvent box. Semiempirical calculations by Extended Hiickel, CNDO, INDO, MINDO/3, MNDO, AMI, and PM3. Originated at Hypercube, Inc. (Dr. N. Ostlund et al.), of Ontario, Canada. Runs under Windows on a 386 or 486 PC and under Motif on a Silicon Graphics workstation. 

King et al. (292)used an empirical binding Ifee-energy function when docking MVT-101 to HIV protease. Forty-nine translation/rota-tions were examined with the Ponder/Richard rotamer library. Only a limited number of retainers for each amino acid were examined Thr(2), Ile(3), Nle(3), Nle(3), Gln(6), and Arg(5). According to the authors, 2.24 x 10 ° discrete states were examined. Sixty-four low ener structures with an average rmsd of 1.36 A were found. If the CHARMM potential was used with the same protocol, then the av-eragQ rmsd was increased to 1.68 A. 

Karplus [166] mented in CHARMM rotamer library with no electrostatics... 

Molecular mechanics, which uses classical mechanics and predetermined force fields to explain the behavior of atoms in molecules. They consider atoms as spheres and bonds as springs. They use an algebraic classical mechanics equation for the energy calculation. The constants in the equation are obtained from experimental data or other calculations and are stored in a data library. The combination of constants and equations is called a force field. These calculations are simple and can be done with many software programs such as AMBER [49] and CHARMM [50]. There are lot of force fields available and some of the popular force fields are UFF [51], MM4 [52], andMMFF94 [53]. 

CHARMM Martin Karplus marci brel.u-strasbg.fr SD, nonlinear CG (FR, and modified PR version, the latter from the IMSL library), Adopted-Basis Newton (ABNR), Newton, truncated-Newton (TNPACK)... 

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