SMOG 2

beta:

• smog_optim module added

2.3:

• 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
• smog_adjustPDB: Added a variety of new options and rigorous residue matching
• 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 in default AA models
• Implemented additional bonded checks in smog-check for supported templates
• Significantly extended smog-check routines

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.