SMOG 2
Version History
- smog_optim module added
- smog_adjustPDB: Added a variety of new options and rigorous residue matching
- Improved error messaging throughout the tools
- Improved ability to introduce non-specific (e.g. CHARMM, or AMBER) terms within a SMOG model
- General clean-up of the code
- Corrected inconsistent use (Gromacs vs. SMOG conventions) when giving specific dihedral angles values in templates
- Fixed bug relating to dihedrals with even multiplicities
- Added -large option in adjustPDB, which allows PDB files to have very large chains (~1 billion atoms and ~15 million residues)
- Fixed a missing bond in DA and DG.
- Implemented additional bonded checks in smog-check for supported templates.
- Fixed minor bug in adjustPDB that prevented RNA tails from being renamed.
- Minor bug, pertaining to placement of ions in smog_ions.
- Performance of smog_ions significantly improved (>1k-fold) for large (>10k atom) systems.
- Added check so only nonbond_params in extras file will be written if they are present in the generated system.
- Corrected issues with definitions of dihedrals in ligands in default models.
- Added more stringent template verification routines.
- Improved robustness of dihedral/angle/bond matching routines.
- Added more tests for dihedral/angle/bond matching routines.
- Added AMP, ADP, ATP, GDP, GTP and extended smog-check for ligands
- Added ability to process single-residue chains with smog_adjust
- Added ability for smog-check to test compatibility with grompp
- Improved error messaging for inconsistent bif-pdb atom naming.
- Added a fix to command line parsing in smog_adjustPDB.
- Significant performance improvements (factor of 3-4) for "vanilla" models and large systems.
- Extended output messaging.
- Introduction to CPAN added to manual.
- Description of force field corrected in manual.
- smog_extract module added.
- Increased default excluded volume in SBM_AA+gaussian, so that it is consistent with SBM_AA.
- Added more checks for mismatched atoms in improper connections.
- Added MIA residue to Whitford09 templates.
- Added connection definition for nucleic to protein (e.g. in aminoacyl-tRNA).
- Removed officially-unsupported templates from distro. Now they may be found in the force field repo.
- Changes option -warnonly to -warn N. Rather than ignore all errors, the first N can be considered warnings. -1 indicates that all errors will be converted to warnings.
- smog_ion module added.
- Cleaned up a variety of routines.
- Added more robust template checks.
- Added -rescaleCD option.
- Improved performance of error checking.
- Minor cleanup of code.
- Added error message when END is missing after ATOM lines.
- Chain ordering in ndx file is now numerical.
- Added free_bond routines.
- Fix to pairType assignment. nbType was used for contact function matching. Now, pairType is used.
- Updated license information.
- Updated warning messages.
- Added additional error checks.
- Initial release of standalone SMOG 2 software package.
Page created and maintained by Jeff Noel and Paul Whitford