#DEFINE FRAGMENT FULL#
Full AMPAC integration if software is installed.Search for conformations using the GMMX add-on.Specify atoms for NMR spin-spin coupling.
Select normal modes for frequency calculations.Include PDB data in molecule specification.Assign fragment-specific charges and spin multiplicities.Define fragments for fragment guess/counterpoise calculations.Manipulate MOs: Select, rearrange/reoccupy orbitals for CASSCF, etc.Set atom equivalences for QST2/QST3 TS optimizations.Specify frozen atoms/coordinates during optimizations.Add/redefine redundant internal coordinates.Constrain to specific space group symmetry.Build unit cells for polymers, 2D surfaces and crystals (periodic boundary conditions).Specify input for complex calculations via simple mouse/spreadsheet operations: Graphical Setup for Specific Calculations Use groups for display purposes and in Gaussian input.Select by PDB residue and/or secondary structure (e.g., helix, chain).Complex filters combining atom type, number, MM settings, ONIOM layer.
Click, marquee, & brush selection modes.Place atom/fragment at centroid of selected atoms.Increase or decrease symmetry of molecular structure constrain structure to specific point group.Rationalize structures with an advanced clean function.Modify bond type/length, bond angles, dihedral angles.Using the bond table and weak bond inclusion.An advanced open dialog, allowing options to be customized and retained across sessions:.Accurately add hydrogens automatically or manually to an entire molecule or a selection.Optionally include intermediate structures from optimizations, scans, etc.Optionally include/discard waters, apply standard residue bonding on PDB import. Convenient palettes for atoms, functional groups, rings, amino acids (central fragment, amino- or carboxyl-terminated) and nucleosides (central fragment, C3’-, C5’-terminated, free forms).Highlight, display or hide atoms based on rich selection capabilities (optionally persistent).
#DEFINE FRAGMENT SERIAL#
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