Release Notes
LocalSCF 2.0 Rev. 2007.08.27
The following bugs have been fixed:
Energy oscillations in QM docking,
Dispersion correction (LJ) was not working in QM docking.
LocalSCF 2.0 Rev. 2007.06.29
Amino acid based selection of SCF and non-SCF parts of molecular structure in QM/QM mode.
Lennard-Jones (LJ) energy correction.
Geometry optimization including LJ term.
DNA and Protein LJ parameters.
Generic ligand LJ parameter assignment based on MMFF atom types.
LJ parameter storage in external parameter file.
Ligand optimization in QM/QM mode in gas-phase and COSMO.
Flexible-ligand high throughput docking in gas-phase and COSMO.
Export of optimized geometry in PDB file.
CM2 and CM3 charges.
Output of Mulliken, CM2 and CM3 charges in MOL2 file.
Ligand conformation generator for ligand bound to protein.
Langevin and NVT Molecular Dynamics of proteins in gas-phase and COSMO.
64-bit support on Linux platform.
LocalSCF2 version 1.0
Support for transition metal systems (d-orbitals).
Transition metal complexes are supported through d-orbital extension of general purpose MNDO, AM1, PM3 and PM5 semiempirical Hamiltonians.
All atom quantum-mechanical modeling of enzymes and DNA - transition metal complexes is made available for hundred thousand atoms systems.
Energy calculation, geometry optimization in gas-phase and solvent environment are supported.
Low resource requirement is provided by the use of localized molecular orbitals for the protein part and delocalized orbitals for the transition metal portion of the system.
Support for DNA/RNA systems.
Computationally efficient initial guess generation for DNA/RNA systems is implemented.
DNA/RNA structure recognition allows reliable identification of structure errors.
Improvements to COSMO solvation model.
New analytical gradients for geometry optimization are implemented.
Support for d-orbitals systems is added.
A considerable speed up is provided for local geometry optimization in solvent environment.
Quantum-mechanical docking and scoring.
High-throughput screening of thousand compounds libraries of drug candidates is implemented.
QM scoring of all atom protein-ligand complexes is provided for gas phase and solvent environment.
QM re-docking of preliminary docked ligands is available through ligand relaxation in the protein-ligand complexes.
Resource saving QM/QM mode allows freezing molecular orbitals of a portion of the system.
General improvements and bug fixes.
New improved initial guess generator.
More reliable SCF procedure.
Automatic control for memory consumption - orbital tidying.
Restart of a terminated job from last saved topology and density matrix.
PDB input/output filter which allows running calculation from an external regular PDB file and saving results in the PDB format.
A powerful Cartesian coordinate - PDB converter is implemented.
Molecular topology input/output filter allows initial guess generation based on the information imported from the external topology file.
Topology preservation mode allows applying restriction to bond breaking/creation.
Bond order analysis for very large systems is implemented.
LocalSCF 2003
Runs on popular PC platform.
Ultra large 100,000+ atoms' protein systems.
Very fast advanced geometry optimization specially tuned for proteins.
Recognition of protein structure from Cartesian coordinates.
Structure quality checking and verification.
Identification of various molecular fragments: amino acid backbone, side-chain, terminal atoms, water molecules, and counterions.
Intuitive and easy for use interface for specification of geometry optimization modes by defining particular fragments or amino acid numbers.
Keyword based recognition and on-fly optimization of drug molecules in the enzyme cavity.
Powerful control options for balancing between speed and accuracy.
Linear scaling COSMO solvation model.
Continuum conductor like screening model implemented.
Small additional resource requirement with the multiplier 2 for memory versus the gas phase mode.
Geometry optimization in COSMO model.
Fast Multipole Method for evaluation of Coulomb integrals.
Assures very low memory requirement, extremely fast calculation of large systems and high accuracy of evaluation of Coulomb interactions.
Provides flexible control over the resource consumption.
True variational linear scalability.
Retains high accuracy for short localized molecular orbitals (the shorter LMOs the less RAM is consumed).
Provides an optimal user-controllable balance between speed and accuracy.
The built-in mechanism for accuracy validation allows comparison of molecular properties in connection with particular keyword options.
Semiempirical Hamiltonians: MNDO, AM1, PM3, and PM5.
