Model Builder
- Sketch, edit and modify molecular structures
- Support all elements on the periodic table
- Build 3D models of liquids, multiple components can be included
- Build fluid interfaces
- Build water/surfactant/oil/vapor interfaces
- Read popular molecular structure files - MOL, MOL2, PDB, GRO, CAR, COR, XSD, XTD
- Editing topology - bond orders, add/remove hydrogen atoms, formal charges
- Group atoms
- Build subsets
- Rest center of mass
- Pack and unpack periodic simulation boxes
- Editing simulation cell parameters
Visualize
- Project management for easy access
- Portable, self-contained project files for easy shearing results with colleagues
- Visual tools - rotate, shift, and zoom
- Display properties of atoms and molecules
- Measure properties - dipole moments, bond lengths, angles, dihedral angles, out of plane angles
- Custom "Look-and-Feel"
Force Field Database (A)
- Each table is a self-contained force field with designated typing rule
- Tables grouped based on force field types (functional forms)
- Multiple tables in the same group can be used in selectable order
- Mix parameters from different tables in the same group
- Version controls of parameters
- Assign atom types, charges and parameters automatically
- Support common force field types - TEAM, AMBER, CHARMM, CFF, DREIDING
- Great coverage for common organic molecules, polymers and drug-like compounds
- Report missing force field terms in molecular structure data.
- Graphic interface for managing database tables
Force Field Database (B)*
- Create new database
- Create or remove tables
- Check-out original parameters from tables
- Check-in (add) new parameters
- Add references, notes of parameterization
- Automatically set version numbers
- Automatic build molecular fragments from missing parameters for parameterization
- Integrate external force fields such as those published in literature
Simulation
- Native energy calculation and normal mode analysis
- Native optimizer
- Native molecular dynamics simulation
- Export simulation files to external simulation engines: GROMACS, LAMMPS, AMBER, CHARMM, DISCOVER and MOE
- Direct graphic interface to run simulation jobs on external simulation engines: GROMACS and LAMMPS
Force Field*
- Open and view force field files
- Preset popular force field types - AMBER, CHARMM, CFF, DREDING
- Supports user-defined force field types
- Import external force field files
- Graphically define atom types
- Spreadsheet editor for parameters
- Assign atom types
- Assign charges
Parameterization*
- Automatic generate conformations for parameterization
- Graphic user interface to Gaussian and GAMESS files
- Standard file format for quantum mechanics data (QMD)
- Support various typing rules
- Automatic build equivalent table to maximize coverage with minimum number of parameters
- Automated procedure for fitting valence, charge and nonbond parameters using ab initio data
- Fit various molecular systems �C single structure, molecules with multiple conformers and molecular clusters
- Fit ab initio electrostatic potential
- Optimize nonbond parameters using MD simulation of liquids
- Automatically validate obtained parameters
- Automatically validation of force field coverage
- Rapid estimate of parameters using atomic properties
- Charge Equilibrium method for estimate charge parameters
- Editable default atomic parameters for estimating force field parameters
User-Friendly Features
- Toolbars for quick and easy access to common commands
- Project tree for convenient organization
- Online document and tutorials
- Supports Windows and Linux platforms
* indicate functions available in Professional version