Software
Conformational Energy Searching
The geometry engines available in SYBYL are primarily focused on conformational energy searching.
Systematic energy sampling of both
acyclic and
cyclic bond rotations is one of the major specialties of SYBYL.
The conformations are sampled over a regular grid of bond rotations. All sterically allowed grid conformations (dihedral angles and molecular mechanics energies, if computed) are archived to an output file. Disallowed conformations are determined using a steric bump check whose tolerance is user adjustable.
The resulting data can be displayed in tabular form via the "Molecular Spreadsheet", and analyzed in various ways, including graphical visualization of computed conformations as well as sorting and plotting of conformational energies.
Molecular mechanics-based energy minimization can also be performed by SYBYL. User specifiable attributes include force-field (AMBER or Tripos), minimization algorithm, and termination criterion. Extensive output is provided during the calculations.
"Sample-Minimize-Filter" is a useful search strategy.
Other programs with geometry/computation engines include AMBER, CAChe, Chem-X, CHARMM, HyperChem, MacroModel, MM2/MM3, and QUANTA. Quantum programs with geometry engines include AMPAC, CHARMM/GAMESS, GAMESS, GAUSSIAN90, and MOPAC.