Semichem, Inc. — Providers of Solutions for Computational Chemistry

Semiempirical Quantum Mechanics

AMPAC™ Graphical User Interface
Features

AMPAC Input

AMPAC 8 Support

Easy and intuitive graphical calculation setup, job submission and result visualization for all AMPAC 8 job types, including optimizations (constrained or unconstrained), frequencies, PES scans ("Reaction Path" and "Reaction Grid"), IRC, annealing, CHN and FULLCHN. Support for nearly all AMPAC 8 models, methods and other input options, including all semiempirical models, all C.I. options, all solvation options and a variety of property options.

Gaussian input

Gaussian Support

Easy and intuitive graphical calculation setup, job submission and result visualization for nearly all Gaussian job types, basis sets and models. Supported job types include optimizations, frequencies, PES scans, NMR and molecular dynamics. Supported basis sets include cc-PVQZ, LanL2DZ, LanL2MB and the Pople basis sets STO-3G, 3-21G, 6-31G and 6-311G (along with support for all appropriate combinations of diffuse and polarization functions). Supported models include the restricted, unrestricted and restricted open-shell variants of Hartree-Fock, LSDA, BLYP and B3LYP, UFF, Dreiding, AMBER, AM1, PM3, MP2, MP4 methods, QCISD, CCSD, CASSCF, G1, G2, G3 CBS-4M, CBS-Q, CBS-QB3, CBS-APNO. ONIOM and PBC calculations are also supported.

Periodic Systems

View, build and edit periodic systems such as polymers, sheets and crystals using AGUI's powerful PBC editor, with built-in support for all lattice types and space groups. Crystal structures can also be loaded from CIF files. Easily create "super cells" for conventional non-periodic calculations in either AMPAC 8 or Gaussian. Ideal for setting up input for Gaussian PBC calculations and visualizing PBC results.

ONIOM

Setup Gaussian ONIOM calculations using AGUI's Layer Selection Tool and powerful Atom List Editor.

Redundant Internal Coordinates

Easily define, edit, read and write redundant internal coordinates and corresponding options for Gaussian calculations using AGUI's Redundant Coordinate Editor.

Visualize NMR Results

Attractive, informative and interactive plots of Gaussian NMR shielding results. Display the atom(s) corresponding to any peak by clicking on the line in the displayed specrtum. Specify and save your own shielding reference values to conveniently convert absolute shielding plots to chemical shift spectra.

AMPAC & Gaussian Input

Visual Active Space Setup for AMPAC 8 C.I. and Gaussian CASSCF

Complete calculation setup and submission for AMPAC 8 C.I. calculations and Gaussian CASSCF calculations, including the ability to graphically select SCF MOs for the active space from AGUI 8's MO dialog.

Multi-Structure Calculation Setup

Automate the tedious task of setting up multi-structure input for AMPAC 8 CHN and FULLCHN calculations and Gaussian QST2 or QST3 calculations.

List Essential Results

Useful summary window presenting essential results from AMPAC 8 and Gaussian output files, in table format.

Visualize Atomic Charges

Display AMPAC 8 and Gaussian atomic charges in molecule view windows by colored atoms based on charges and/or by labeling the atoms with scalable numerical text. Supported atomic charges include Coulson, Mulliken and ESP for AMPAC 8 and Mulliken, ESP, APT, NBO and AIM for Gaussian.

Molecular Orbitals Levels

Powerful MO dialog for easily and quickly viewing MO energy diagram(s) and corresponding MO surfaces.

Visualize Surfaces

Display a variety of isosurfaces or mapped isosurfaces in solid, mesh or transparent format using a seamless interface with AMPAC's acubegen and Gaussian's cubegen utilities. Available surface types include MO, total electron density, alpha electron density, beta electron density, unpaired spin density, ESP, current density magnitude and NMR shielding. Any of these functions can be mapped on the surface of another, for example ESP values can be mapped onto a total electron density isosurface or NMR shielding values mapped on a current density magnitude isosurface. Surfaces are displayed in molecule view windows together with corresponding structure.

Interactive 2D and 3D Plots of Multi-Structure Results

Attractive, informative and interactive spectra-like plots for all multi-structure results, including AMPAC 8's reaction path, annealing, CHN, FULLCHN, IRC and reaction grid (3D plot) results. Gaussian's scan, IRC, molecular dynamics trajectory and optimization results may also be displayed. Easily switch between molecules in a group by selecting corresponding points on the plot.

Visualize Vibrational Spectra

Display interactive IR spectra (including line shapes and widths) from both AMPAC 8 and Gaussian vibrational frequency calculations. Raman and VCD spectra are also available for display with Gaussian calculations. Easily switch between normal modes displayed in a view window by selecting corresponding peaks in the spectra.

Visualize Normal Mode Vibrations

Visualize normal mode vibrations along with corresponding displacement vectors and dipole derivative vectors in molecule view windows.

Ease of Use/ Convenience/ Common tasks

Calculation Schemes

Save an unlimited number and type of AMPAC and Gaussian calculation setup "Schemes" (named keyword combinations), for quick-and-easy launching of similar calculations.

Quickly Launch Calculations

Easily launch AMPAC 8 or Gaussian calculations on any molecule with any calculation setup "Scheme" with one click of the mouse using AGUI 8's Quick Launch The corresponding results will be automatically loaded when the job is complete.

Job Management

Manage all AMPAC 8 and Gaussian jobs submitted from AGUI 8, including streaming output files of running AMPAC 8 and Gaussian jobs to a display window for real-time monitoring of job progress.

File Compatibility

Load structures and other data from a variety of file types, including all AMPAC 8 and Gaussian file types, MDL Mol, Sybyl Mol2, PDB and Crystallographic Information Files (CIF). Multiple files can be opened simultaneously.

Save Files

Save structures as AMPAC 8 input, Gaussian input, MDL Mol files and Sybyl Mol2 file formats.

Point Group Symmetry

Easily view the approximate and exact point group symmetry of displayed structures. The molecules can also be symmetrized exactly and geometry changes constrained.

Build Molecules From Fragments and Atoms

Easy, chemically intelligent point-and-click building of molecules in 3D view windows using AGUI 8's periodic table along with a variety of built-in, pre-optimized fragments. Users can also create custom fragment libraries. Fragments in molecule view windows can also be dragged-and-dropped for chemically intelligent building.

Easily Add Hydrogens and Delete Atoms

Easy point-and-click deletion of atoms and addition of hydrogens, as well as automatic, accurate addition of hydrogens to whole structures. This is especially useful for structures obtained from PDB files).

Undo / Redo

Unlimited Undo / Redo when building or editing structures in any way.

Easily Edit Molecular Geometries

Easy point-and-click editing of molecular geometry and bonding (including point group and space group symmetry constraints) using the powerful bond, angle and dihedral Semichem Smartslides™.

Edit Atomic Properties

Molecular Spreadsheet™ display and editing of a variety of atomic properties, including element, Cartesian and internal coordinates, Z-matrix connectivity, optimization flags, fractional coordinates for PBC, Oniom layer, Molecular Mechanics atom types and more. Multi-row editing is supported.

Multiple Molecules and Molecule Groups

Work with multiple molecules and molecule groups simultaneously. This is especially useful for comparison of structures and results, copying structures or bonded substructures between windows. It also facilitates set up of multiple geometry input and output to and from AMPAC 8 and Gaussian.

Convenient User-Interface

Multiple ways to carry out any desired action, including from the AGUI 8 main menu bar, tool bars or from right-click contextual menus in any molecule view window.

Preferred Settings

Save most AGUI 8 settings as preferences to be used upon subsequent AGUI 8 launches.

Desktop Integration

Easily load one or more recognized files into a new or existing AGUI instance from the command-line, by double-clicking on the desktop or in the Explorer/Finder window. Copy and paste by dragging and dropping files either onto AGUI 8 icons or onto any AGUI 8 view window.

Active Maintenance and Development

AGUI (along with AMPAC) is constantly being improved (also see here for changes made since AMPAC 8 was first released) in response to customer feedback, market demands, new ideas and methods in the literature, changes in the computing landscape as well as the interests of our own researchers and collaborators.

Compatibility

Open Files

Load structures and other data from a variety of file types, including all AMPAC 8 and Gaussian file types, MDL Mol, Sybyl Mol2, PDB and Crystallographic Information Files (CIF). Multiple files can be opened simultaneously.