AGUI Features

Build Molecules in 3D

Start with pre-minimized fragments for functional groups, rings, ligands, amino acids, RNA/DNA bases
Adjust your structures using Semichem's chemist-friendly SmartSlide™ that lets you move atoms around through bonds, angles and dihedrals, the way you think.
Establish and manage custom fragment libraries
Multiple levels of UnDo/ReDo for easy editing of structures
Unique Z-matrix editor for complete control of geometry
Redundant Coordinate Editor
Atom Group, Atom List and Atom General Selection editors for easy selection and management of subsets of atoms
Multiple molecule views for working with different molecules at the same time

AMPAC & Gaussian Calculation Setup and Management

Comprehensive Calculation Setup Dialog Boxes

Virtually every option and type of calculation available in AMPAC 10 and Gaussian can be defined and accessed from this dialog box. Its is also "smart", and will change dynamically to only present those items that are compatible with the options you have already selected. Context-sensitive help is available for AMPAC options.

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

Complete calculation setup and submission for AMPAC C.I. calculations and Gaussian CASSCF calculations, including the ability to graphically select SCF MOs for the active space from AGUI MO dialog.
Job 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, all managed by a flexible and powerful Schemes Editor.

Quickly Launch Calculations

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

Job Management

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

Visualize Calculation Results

Quick View of Results

A useful summary window shows just the essentials in tabular form.

Visualize Atomic Charges

Display atomic charges in molecule view windows by colored atoms based on charges (Numerical values are also available. Atomic charge types include Coulson, Mulliken and ESP for AMPAC and Mulliken, ESP, APT, NBO and AIM for Gaussian.

Molecular Orbital Level and Shape Viewer

Powerful MO dialog for easily and quickly viewing MO energy diagrams and the corresponding MO shapes.

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. AGUI will now plot surfaces that result from performing operations on cube files from both AMPAC and Gaussian, such as adding and subtracting.

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

Attractive, informative and interactive spectra-like plots for all multi-structure results, including AMPAC'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 and Animate Vibrations

Display interactive IR spectra (including line shapes and widths) from both AMPAC and Gaussian vibrational frequency calculations. Raman and VCD spectra are also available for display with Gaussian calculations. Easily switch between vibrations displayed in a view window by selecting corresponding peaks in the spectra. Static displays of vibrational motions can also be shown using vectors.

Display Dipole Moment Vector

The overall dipole moment for a molecule may be represented by a single arrow superimposed on the 3D molecular structure.

Mapping of 2D Surface Contours

Isovalues from any cube file for any property can be mapped as a series of contours onto a user-defined 2D plane.

Positioning of Molecules

These new tools are part of the main window and position molecules precisely in the View Window.
Customize The Appearance of Plots and Spectral Displays

A variety of labels can be added or changed on various plots.

Display Molecular Properties on Plots

Values and labels for properties can be added to the View Window.

Display Two-Coordinate Reaction Results

A 3D surface is plotted where two axes are the reaction coordinates and the third is energy.

Movies!

Animations of vibrations or reaction progress can be save as GIF movie files.

Stereochemistry

The absolute configuration for each chiral center (automatically detected) in the molecule can be displayed

Ease of Use & Convenience

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.

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 and Gaussian.

Convenient User-Interface

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

Interface Customization

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

Active Maintenance and Development

AGUI (along with AMPAC) is constantly being improved (also see here for changes made since AMPAC 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 and Gaussian file types, MDL Mol, Sybyl Mol2, SDF, pdb and Crystallographic Information Files (CIF). Multiple files can be opened simultaneously.

Save Files

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

Powerful Tools for Manipulating Protein Data Bank Files

New capabilities for dealing with pdb files have been added including multiple options for setting input options, comprehensive new dialog boxes for selecting residues and secondary structures.

Publication Support

OpenGL 3D Graphics

High quality OpenGL-based 3D views of molecules or molecule groups in a variety of customizable view formats, including user-scalable text for atom symbols and number labels.

Save High-quality Images

Save molecule view window images to the system clipboard or a variety of image file including TIFF, JPEG, PNG, PNG, BMP and EPS.

Specific Gaussian Support

General

Easy and intuitive setup dialog box, job submission and visualization of results for nearly all Gaussian jobs, including optimizations, frequencies, PES scans, NMR and molecular dynamics. Supported basis sets include commonly-used Pople-type, 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 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.