Gmx-mmpbsa

Fixes¶
- fixed Boltzmann constant for IE
- fix the ligand mutation
- fixed analyzer error when interval > 1
- fixed residue selection within
- fixed ChainID assignation when no reference structure is defined
- fixed the selection to print when decomposition

Additions
* **Now, gmx_MMPBSA is in Zenodo [](https://zenodo.org/badge/latestdoi/295050575). You can refer to us in this way in what we publish the article**
* Added Interaction Entropy to gmx_MMPBSA output file
* Added a new class to save IE in a csv file
* Added "Go to Top" button to documentation HTML.

Fixes
* Error when ligand and/or receptor are discontinuous (Testing it)
* Error when ligand and/or receptor are discontinuous and numbered non-consecutively
* Non-critical errors and inconsistencies in documentation

Changes
* `receptor_mask` and `ligand_mask` have been removed from input file variables. Now we extract the amber mask directly
based on the GROMACS index file
* The receptor and ligand mapping in the complex was improved. Now we use a method based on the GROMACS index file
* The method `Map` of the `system_MMPBSA` class has been restructured. Now always processes amber masks
* Changing the IE calculation function to a class

Additions
* New variable (`overwrite_data`) to overwrite gmx_MMPBSA data.
* More informative message when sander fail. Useful for PB calculation

Fixes
* Protein-ligand with charmm force field example
* Stability calculation
* gmx path error
* leaprc.GLYCAM_06h-1 file
* Protein-glycan example

Changes
* Documentation banner

Additions
* Documentation at Github pages
* Charmm force field support
* Amber topology generation from GROMACS topology. Work for Charmm and Amber force fields
* New flag for topologies (`-cp`, `-rp` and `-lp`) added
* Now `gmx_MMPBSA` supports discontinuous receptor and ligand.
* Glycine scanning
* Autocompletion script for both `gmx_MMPBSA` and `gmx_MMPBSA_ana`
* Versioneer to control the semantic version.
* Argument type checker for the command-line

Fixes
* Alanine scanning tutorial
* GROMACS executable path
* The `-gui` option has been changed by `-nogui` and fixed when it is defined
* Improvement on documentation

Changes
* Documentation theme. Now we use Material
* Alanine scanning variable. Now `mutant` correspond to mutant amino acid (ALA and GLY)
* The `gmx_MMPBSA_gui` was changed by `gmx_MMPBSA_ana`
* Improvement on the topologies construction process
* Order in which the trajectories are cleaned. Now, the topology is built and finally, the trajectories are cleaned

**Improvements**
- More comprehensive output log file
- Best handling of structure files

**Additions**
- New ligand force field (Zwitterionic aminoacids)
- A new flag (-cr) added for defining a reference structure (guarantee a better consintency in generated PDB files)
- API documentation

**Changes**
- `gmx editconf` is used to generate PDB files instead of `gmx trjconv` (14)
- gmx_MMPBSA data is copied in AMBER as an independent folder
- `*gro` files can be used as a MD Structure+mass(db) file
- Updated tutorial list in README ([Protein_DNA_RNA_Ion_ligand BFE calculations](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/test_files/Protein_DNA_RNA_Ion_ligand))

- [x] Support various metallo-complexes formats
- [x] New tutorial added (see [Protein_DNA_RNA_Ion_ligand tutorial](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/test_files/Protein_DNA_RNA_Ion_ligand))
- [x] Keep all the temporary files in the folder for debugging purposes

v.1.1.0
In this version, we have changed and implemented several functions:
- [x] Now supports carbohydrates as ligand. See this [tutorial](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/test_files/Protein_glycan)
- [x] Now supports metalloprotein-ligand complexes. See this [tutorial](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/test_files/Metalloprotein_peptide). (it has limitations, see [issue](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/3))
- [x] We changed the notation of the force fields, now the user can define any force field (We have only tested Amber and GLYCAM force fields) available in AmberTools. Charmm is not yet supported. See this [section](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA#input-and-output)
- [x] We have added data folder to gmx_MMPBSA module. This folder contains the GLYCAM_06h-1 force field files (Compatible with amber99sb and early, see at [http://glycam.org](http://glycam.org/docs/help/2014/07/02/which-protein-force-fields-are-compatible-with-glycam/)) which is not in AmberTools.