SMOG 2

Version History

SMOG 2 updates are documented here. The version history for the Shadow Contact Map can be found elsewhere. Since new versions occasionally have bug fixes, it is highly recommended that you only use the most recent released version. If you would like to test out the newest options available, then you may be interested in trying the beta version.

Beta:
- 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.
2.2:
- 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
2.1:
- 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.
2.0.3:
- Added -rescaleCD option.
- Improved performance of error checking.
- Minor cleanup of code.
2.0.2:
- 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.
2.0.1:
- Updated license information.
- Updated warning messages.
- Added additional error checks.
2.0:
- Initial release of standalone SMOG 2 software package.

Page created and maintained by Jeff Noel and Paul Whitford