QuantumBio has released an update to DivCon6. This new version adds some key features to the software and addresses requests of current users. If you would like to explore the use of the software in your own structure based drug discovery efforts, contact firstname.lastname@example.org or visit our licensing page.
DivCon6.0.5 Build-1997 – April 15, 2014
- Correct treatment of false atom radicalization due to pre-refinement structural inconsistencies, “hot spots” and other issues. This problem had lead to complaints of “odd number of electrons” in previous versions even when the chemistry was correct.
- Acceptance of non-integer values for memory options in MOE/DivCon and Phenix/DivCon. In prior versions, the user would need to make sure that the memory value was a whole number.
- More accurate memory prediction both in Phenix/DivCon and in SVL. This information is also provided as part of the screen output during the calculation.
- Additional phenix.log warnings and information concerning memory requirements for optimal performance. If there is less memory available than optimal, the simulation will still proceed – albeit at a slower pace.
- Updated SVL for better preparation (along with new documentation of the same to be posted on http://quantumbioinc.com/products/phenix-divcon/ tutorials and case studies).
- Updated csh environment scripts. In previous versions, using the csh script would lead to spurious object file linking of non-QuantumBio software. Note: due to limitations in CSH/TCSH, the location of $QBHOME is fixed at installation and this qbenv.csh file will need to be updated in the event that $QBHOME is moved.
- Updated moe-menus file to remove outdated or obsolete functionality.
- BETA: Updated symmetry calculation for additional space groups available in non-regional/full refinement. For examples and information, contact email@example.com
- BETA: Interaction energy calculation and decomposition (e.g. Eint, Epol, Ees, and Ect) available on qmechanic command line. In the coming weeks, documentation and examples will be provided at http://quantumbioinc.com/products/target-ligand-interaction-profiling/
DivCon6.0.4 Build-1947 – March 27, 2014
- Bug Fix: In previous versions, the gradients for protons remained unused in the refinement leading to poor proton refinement.
- PDB File Support: Improved PDB parsing for unusual atom names.
- PDB File Support: Added processing for HELIX and CRYST1.
- Added the –repo option to qbphenix command line to allow for internal pdb/mtz repository.
- New script and PBS template to be used as an example in running a large set of PDB structures.
- Added qbLigandInteractions.svl file for MOE interface in order to generate ligand interactions diagrams (and analyses) automatically for pre- vs. post- refinement structures.
- NEW Functionality (BETA): Symmetry has been added optionally when running full structure QM refinement (not available on regional refinement).
- Improved error trapping for Phenix/DivCon including more accurate treatment of errors within the QM-region.
- General maintenance release primarily consisting of “under the hood” performance improvements.
- NEW for DivCon6 (!!): Updated pairwise energy decomposition (QM-PWD) command line-based functions – MOE interface coming soon!
- NEW for DivCon6 (!!): Semiempirical QM-based nuclear magnetic resonance (QM-NMR) command line – MOE interface coming soon!
- Overhauled thread system in order to maximize performance in multi-core environments.
- Overall performance improvements.
- Updated Phenix log feedback during refinement.
- Completely updated Phenix/DivCon tutorials!
- Bug fix: addresses occasional/intermittent segfault associated with specific types of ligands in refinement.
- Bug fix: addresses segfault when calculating ligand strain on a single metal ion.
- Updated phenix.log output to provide additional information about the core QM region along with the buffer QM region.
- Increased speed and parallelism associated with the calculation of QM gradients.
- Assorted perception and protonation fixes.
- QBReporter improvements to process the h5 file and output the PWD, charges, and PDB geometries.
- Complete overhaul of DivCon package using modern, high-performance design.
- Pervasive, thread-based parallelism applied throughout the software.
- Vastly improved SCF convergence both for linear scaling and for non-linear scaling techniques.
- Implementation of AM1 and PM6 Hamiltonians for energy, PWD, and X-ray refinement.
- Advanced nuclear magnetic resonance (NMR) capabilities for calculation of chemical shift and chemical shift perturbations.
- Shipping integrations for both MOE (for NMR and modeling) and Phenix (for X-ray).