Issues and History/Change Log

Known Issues - To-do List

Planned features/fixes (short-term)

  • (Fixed in v1.1.0.hf1) gRINN fails to process GROMACS-generated TPR files in which no chain ID is present. This appears to be the case where only a single protein chain is included. This will be fixed in the next version.

  • gRINN log file will include parameters used when calling gRINN.

  • (Fixed in v1.1.0.hf1) gRINN fails to display IEMs and RCs for proteins with less than 100 amino acids. This will be fixed in the next version.

  • gRINN will let the user export computed shortest paths list.

  • Exported networks will include better residue labeling instead of simple integers.

  • NAMD won’t be spawned multiple times, letting the user give as input larger DCD files and avoid insufficient memory errors.

  • Input file window will be simplified, avoiding the confusion on file types for NAMD/GROMACS data.

  • Switching will be optional for NAMD-type data, as opposed to the current implementation (off)

Planned features/fixes (longer-term)

  • Support for non-protein residues (organic ligands, lipids, nucleic acids).

  • Chain ID requirement on input files should be removed. We are working on code to relax this requirement.

  • View Results UI will allow visualization of Electrostatic and vdW energies separately, in addition to separate network analysis features.

  • A windows-compatible version is on the way.

Planned features/fixes (unlikely to implement in foreseeable future)

  • Support for AMBER-generated trajectories.

v1.1.0.hf1 (2018/06/21)

This hf (hot-fix) version fixes two bugs which rendered gRINN unusable in some cases and an addition to sample input files:

Bug fixes:

  • A major bug in gRINN which leads to a failure in processing TPR files without chain IDs is corrected. gRINN will assign a default chain ID of “P” to residues which have no chain IDs assigned in input TPR.

  • IEM annotation is now shown only for smallest proteins (with sizes of at most 20 amino acids).

Additions:

  • charm27.ff files (used by GROMACS sample trajectory data) are included in the distribution (considering that this force-field may not be included in GROMACS installation of some users).

v1.1.0 (2018/04/06)

This version introduces a major internal code rehaul, leaving major features of gRINN unaffected. There are additional new features as well as major/minor bug fixes:

New Features:

  • A new calculation setting for non-bonded interaction cutoff for NAMD simulation input is introduced. In the previous version, filtering cutoff distance parameter specified both the filtering cutoff distance itself and the non-bonded interaction energy cutoff for NAMD simulation input.

  • gRINN now supports Charmm simulation input as well.

Major/minor bug fixes:

  • A bug which caused faulty reading of more than one parameter file for NAMD simulation input is fixed.

  • A minor bug which caused incorrect protein structure display upon start of View Results interface in Mac OS version is fixed.

v1.0.1 (2017/12/27)

Initial release of gRINN.