CAChe 6.1.12
New in the release:
A new license key is required to install release 6.1.12.
New property, electrostatic potential on van der Waals surface, provides more intuitive coloring for electrostatics. Red indicates the most positive areas and blue indicates the most negative areas, similar to the colors on the terminals of your car battery.
New optional Spartan style coloring for electrostatics that can be selected at the bottom of the Tabulator Settings panel.
The latest MOPAC version: MOPAC 2002 v2.5.0.
New “LAST” keyword recovers the previous MOPAC settings used on a chemical sample. It has been added to the standard procedures for the verify transition state and find reaction paths Workspace experiments, that are found under Property of: reaction and transition states. After refining a transition state, it is important to use exactly the same method (e.g., PM5), multiplicity and solvent field settings, etc., for these two subsequent steps. However, it is all too easy to not do so, leading to erroneous results. Now, when these experiments are run, these standard procedures automatically use exactly the same settings that were used in the last calculation on the chemical sample, minimizing the possibility for error. If the last calculation was not a MOPAC calculation (Tabulator calculations are ignored and skipped over), then the standard settings are used.
The default setting for the solvent effective radius (RSOLV) in all MOPAC procedures using COSMO simulation in water has been changed from 1.0 to 1.3 A, as recommended in the MOPAC manual.
MOPAC keywords are now printed to the Workspace Experiment Status window at the start of a MOPAC calculation, allowing users to verify the settings immediately, without waiting until the end of the calculation.
New, improved MOPAC PM5 parameters for Ti, Cr, Fe and Cu, labeled “Fujitsu, October 2004”.
New MNDO, AM1 and PM3 parameters, completing all of the main group elements.
New, more accurate, polarizability calculations in MOPAC for H, C, N, O, F, Cl, Br and I.
New MOPAC procedures added to ProjectLeader to calculate polarizability (previously, only DGauss procedures were available).
All regression analysis tools in ProjectLeader now use the same method to calculate r(CV)2, allowing direct comparison of results from different analyses.
The keywords CUTOF1 and CUTOF2 have been added to all procedures involving MOZYME geometry optimizations. These cutoffs control how various one- and two-electron integrals and electrostatics are computed. They have been added with a reduced value of 7 A, which will result in faster calculations without significantly affecting the accuracy.
The keywords OPT_TYPE LENIENT and MICRO 1 have been added to all procedures involving DGauss geometry optimizations. To determine the optimal step length to take along the direction of the displacement vector, the DGauss geometry optimizer by default performs a line minimization in this direction. If it cannot find a point on this line at which the energy is lower, the optimizer will fail. This can especially be a problem if the potential energy is flat since the noise in the numerical algorithms employed within DGauss can obscure the search for an optimal geometry. Previous DGauss versions did not use a line minimization. These keywords disabled the line minimization and allow DGauss to reliably optimize geometries.
A general warning now appears when users try to open or save non-CAChe files to alert the user to check the chemical sample. For example, in certain circumstances the SYBYL MOL and MOL2 file translators may incorrectly assign atom charges.
The following enhancements are specific to the ActiveSite add-on to WorkSystem Pro:
All docking experiments return a map containing some of the lowest energy poses.
Co-crystallized ligands present in the PDB file are returned in the maps containing the best docked poses.
Enhanced PMF protein atom-typing now correctly designates sulfur as a hydrogen bond donor, even when hydrogen atoms are not added.
The Workspace Dock into Active Site window and the Workspace and ProjectLeader Experiments now use a consistent set of default settings for FastDock.
Two new ligand-protein docking properties have been added to ProjectLeader: score a ligand's currently docked geometry and optimize a ligand's currently docked geometry. These complement the existing property, dock a ligand into an active site.
The Workspace docking experiments have been reorganized to be consistent with those in ProjectLeader.
Fixed in the release:
Several bug fixes to the IR spectral tool.
