Unix workstation platform user, visualizes results that can be displayed across
many computer platforms including Macintosh and Windows.
SemiChem products are available at http://www.semichem.com. AMPAC TM ,
available as a stand - alone product with Windows - based and workstation level
interfaces, is a semiempirical quantum mechanical program featuring SAM1,
AM1, MNDO, MNDO/d, PM3, MNDO/C, MINDO/3 semiempirical methods.
AMPAC TM also includes a graphical user interface (GUI) that builds mole-
cules and offers full visualization of results. The SYBYL/Base TM program
offered by Tripos, Inc. (products described below) provides an interface with
interactive graphing and structural display tools that can be used to access
AMPAC ’ s calculation tools.
Serena Software, Inc. at http://www.serenasoft.com has released PcModel
9.1. The program supports OpenGL rendering of molecules (high - quality
graphics), as well as the Q - Chem ab initio quantum chemistry program. Geom-
etry optimization is available using a wide variety of force fi elds — MMX,
MM3, MMFF94, AMBER, or OPLS - AA — and includes a central force fi eld
model for organometallic molecules. One can carry out conformational search-
ing using any of the included force fi elds, as well as compute normal vibrational
modes. PcModel 9.1 interfaces to many quantum chemistry programs includ-
ing Gaussian, Gamess, PQS, ADF, Turbomole, and Q - Chem and can read from
and write to many types of chemical information fi les including: PDB (Protein
Data Bank), SDF, MM3, Macromodel (Schrodinger, Inc.), SYBYL (Tripos,
Inc.), Alchemy (Tripos, Inc.), MDL - Mol, Gaussian (Gaussian, Inc.), Gamess,
Jaguar, MOPAC, AMPAC, Hondo, ADF, PQS, Turbomole, Chem3D (Cam-
bridgeSoft), Tinker, and Smiles. Transition metal complexes can be built with
explicit sigma bonding, lone - pair coordination, and pi - system coordination.
Parameters are available for all transition metals. The software is supported
on Macintosh, Windows, and Linux platforms.
Tripos offers a wide array of computational and modeling software
programs available at http://www.tripos.com/index.php?family=Modules,
SimplePage,discovery_info. Those of most interest to bioinorganic chemists
are described briefl y here. The SYBYL/Base TM program includes a compre-
hensive set of molecular modeling tools for structure building, optimization,
comparison, visualization of structures and associated data, annotation, hard -
copy and screen capture capabilities, and a wide range of quantum mechanical
methods and force fi elds. Its use requires a workstation environment. The
SYBYL/BaseTM program includes implementations of the AMBER united -
atom and all - atom force fi elds as well as MMFF94 and AMPAC (SemiChem).
In late 2006, Tripos offered SYBYL TM 7.3. In its advanced protein modeling
section, the software suite provides researchers with protein homolog
searching, sequence alignment, and comparative modeling capabilities. A new
graphical interface provides a streamlined workfl ow while allowing expert
users full control over the protein modeling and refi nement process. Other
improvements in the suite will be of interest in protein informatics and
modeling.
COMPUTER SOFTWARE FOR CHEMISTRY 179