Webtool history

Since SMOG2 is now available, the web version of SMOG is no longer under development. We will fix bugs, if they are found. If we update the force field generation code, it will be documented here. Resolved technical issues are described at the bottom of this page.

Updates

Resolved Technical Issues

December, 2021 Resolved an issue on the backend of the SMOG server that was not allowing errors messages to be redirected to screen. This did not affect any force field files generated. However, if SMOG quit before generating the output files, cryptic error messages were being shown.

November, 2020 We finally implemented proper SSL certificates, so smog-server is now secure. During this transition, the smog-model generator and shadow-map tool were temporarily unavailable. We believe the migration is complete, but please let us know if you see any unexpected behavior with the site.

September 10, 2018 There was an unexpected few-hour interruption of service due to server maintenance. All services have been restored.

May 30, 2018 The server was offline for scheduled hardware migration. Service has been restored.

July 12th, 2016 The server was intermittently unavailable due to routine maintenance.

April 29th, 2016 The server was temporarily unavailable for a few hours today.

July 16th, 2014 Contact map options were inaccessible in v1.2.2. Options are re-enabled.

April 22st, 2014 The server was taken down for unexpected maintenance. Service was restored after a few hours.

September 10th-11th, 2012 During migration and upgrade to smog-server.org, there were intermittent interruptions in service. Thank you for your patience during this transition.

December 12th-13th, 2011 Due to a server update, there was a brief interruption of SMOG availability. If you tried to generate a model during this period, you would have received a fatal error, even if the pdb file was formatted properly.

November 4th, 2011 For V<=1.0.6, if two atoms are too close, then they were omitted from the 'exclusions' list, which results in a slightly larger repulsive interaction between these atoms. This only happened if two CA atoms are closer than 2 Å (in the CA model) or if two atoms are within 1.5 Å (AA model). This has been resolved for V>=1.1.

July 5th, 2011 For Versions <=1.0.6, if you were to supply a contact map and one of an atom in a contact is not supported by the smog webtool (possibly due to misnamed atom in the pdb file), a warning message was issued, but the webtool did not return a fatal error. While a fatal error was not reported, it was possible that the force field may contain errors due to this. For V >=1.1, this warning is now a fatal error.

January 10th, 2011 There were cases where Shadow was treating DNA like protein and excluding residue i from having contacts with neighboring residues i-3 < j < i+3. This behavior is undesirable since nearest neighbor stacking interactions are important. DNA no longer excludes neighboring DNA residues from having contacts. RNA was already handled correctly.

December 25th, 2010 The contact to dihedral ratio was being calculated for the whole system, including ligands. Now, the contact/dihedral ratio is maintained for the protein/na system, excluding the ligand. So, if you prepare the same system with and without the ligand, the only difference in the .top file will be the terms for the ligand.

December 14th, 2010 There was an issue with the scaling of contacts to dihedrals for RNA. It appears to have been introduced on October 19th, 2010. If you generated RNA force fields in this period, then this ratio may not be exactly what you indicated on the interface. If this ratio is important for the particular system you are studying (in many cases the results are insensitive to this value), it would be worth double checking that the total contact energy and total dihedral energy are appropriately scaled. Proteins and DNA were unaffected. We also changed the code so that the ratio of energies is preserved, even if you have missing atoms. Before, if you had atoms missing in your system (such as OXT atoms), then this ratio was perturbed as well (for this reason, it was always stressed to check your files, especially the output files).

June 16th, 2010 System maintenance resulted in a temporary interruption in service.

May 20th-June 1st, 2010 There was a temporary issue with generating CA-models for proteins with multiple chains. Functionality has been restored.

May 19th, 2010 2 energetic misassignments were identified and fixed for RNA/DNA. The bond angle for atoms C3*-O3*-P(i+1) was assigned twice. A rigid dihedral angle about the C5-C6 bond in A and G was assigned twice. Both assignments were corrected.

September 29th, 2009 A bug was identified and fixed: When using a CA model and uploading your own contact file, incorrect values were used for the excluded volume. All other combinations of models and contacts were unaffected.

September 28th/29th, 2009 Temporary issue with contact map calculations resulted in all generated files using a cut-off contact map with all-atom representation. If you calculated a .top and .gro file on these two days, double check your files.

August 24th/25th, 2009 Web page intermittently unavailable due to unexpected server issues. Functionality restored.

August 10th, 2009 A precision issue was fixed. For shadow contact calculations, we now use precision of 0.01 Å for coordinates. For technical reasons, we still use 0.001 A precision for coordinates when calculating cut-off contact maps. This difference will be resolved soon.

Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford