Suggestion to include features in next version release

[Gsk468]

Dear Developers,
Thanks for creating this awesome and useful tool. Here are a few suggestions, if you can include them in the next version release of Streamd:

1. The terminal doesnot show the status of the steps running in the terminal for the equilibration and production runs just like that is visible with verbose (-v) in Gromacs. It is to be checked from the log file of production run to check the number of steps run.
2. It will be good to show the % value of occupancy for each interaction on the image in PLIF_occupancy.html.
3. Will be appreciated if the option to change the font/label color and size/bold for plif.png and plif_framemap.png.
4. The mmgbsa/mmpbsa script is generating only FINAL_RESULTS_MMPBSA_03-12-2024-15-24-52_1bfca90f4f206d26.csv and FINAL_RESULTS_MMPBSA_03-12-2024-15-24-52_1bfca90f4f206d26.dat files but not the plots that can be generated with gmx_MMPBSA_ana tool (like residues contribution, interactions over frames etc). Also the other files are not been saved so that it can be analysed using gmx_MMPBSA_ana tool itself.
5. How to set the index values for MMGBSA/MMPBSA calculation using streamd when the system has multiple ligands (for example a ligand and NAD as cofactor) and binding affinity between protein-ligand and protein-cofactor has to be calculated?
6. For some reason itis giving error when using save_traj_without_water option (run_md: error: unrecognized arguments: --save_traj_without_water). Even when typing run_md -h option, it doesnot show save_traj_without_water option.

[avnikonenko]

Hello!
Thank you for your suggestions! We will try to implement it very soon.

1. The idea was to avoid overloading inexperienced users with technical information while redirect such details into separate log files for the advanced usage. As I understand, you could find this information in the specific log files?
   Although we can add -v option into run_md module, which would allow the tool to show all information both in the terminal and as it was before still save it into specific log files. Would such option solve this small issue for you?

2. and 3. Seems easy to add to the next release.

4. For sure, will be useful to implement it. Although it will require a little bit more time than other improvements.
5. --ligand_id and --append_protein_selection arguments can be used in this scenario. To calculate the affinity between a protein-cofactor system and a ligand, use --ligand_id 'UNL' (set as the ligand group id from gmx make_ndx -f solv_ions.gro -n index.ndx list of groups, StreaMD uses 'UNL' as the default). Additionally, specify --append_protein_selection 'NAD' to include cofactor into the protein system for the calculations.
   To calculate energy for the protein system and the cofactor, use --ligand_id 'NAD' instead.
6. Try to remove the current installation and reinstall using: pip install git+https://github.com/ci-lab-cz/streamd.git
   New features sometimes are not released into the pip version immediately.

[Gsk468]

Thank you for your prompt response. Point 6 is resolved on updating the package.
There is another point to mention: while using run_prolif module, the calculation is running only on 1 core of cpu while my system has 32 cpu, 64 cores. I am using the command: run_prolif --wdir_to_run /home/gsk/Documents/RUN-TEST/md_files/md_run/output -c 64 -v . Any help regarding this?

[avnikonenko]

This issue (#30) has been just solved, it should be resolved now while you have updated the package. In short, while the --ncpu argument parallelizes the tasks on the multiple ligand level (1 core per each ligand and run all calculations simultaneously), the --n_jobs argument is needed if you want to use multiple cores per ligand.

[avnikonenko]

Also, regarding the point 5.
Make sure your cofactor has indeed "NAD" Group ID. In StreaMD, by default, all cofactors get a new unique residue ID to avoid potential problems in case of multiple cofactors. You can check it in /home/gsk/Documents/RUN-TEST/md_files/md_run/output/all_ligand_resid.txt file. I will add this info into README for other users.

[Gsk468]

--n_jobs worked like a charm. Thanks.

[Gsk468]

Hi, is there a way to make triplicate runs of the simulation via command line using streamd, or do we have to repeat the whole process thrice to run the triplicates of the same complex? Also, do you plan to include a feature for analysis of replicate trajectories? Thanks.

[avnikonenko]

Hello! You can check the solution in issue #35. Hope it will work well for you!

[Gsk468]

HI,
In the point 4 of the first comment, I updated to the latest version of streamd and during gbsa calculation I can see the temporary folder while it is running but it gets deleted once the calculation is over. Is there any option to retain that temporary folder having all the generated files of mmgbsa in order to open it with gmx_MMPPBSA_ana and save the per-residue contribution plots?

Also in the prolif section you mentioned that font size can be altered, but i couldnot find that option. Can you please mention how to bold and increase the font size of labels on generated prolif plots (currently they are very small and light) ?

Thanks for your efforts.

[avnikonenko]

Hello!

1. I just have added a new argument --debug for run_gbsa.
   Please update it through pip install git+https://github.com/ci-lab-cz/streamd.git and run run_gbsa as usually with --debug argument. In the logging you will see the temporary directory path, which won't be deleted if the argument is used.
2. There is no option to change bold font, but you can change the --base_size and --point_size in prolif_drawmap and prolif_draw_by_frame (special tools, which more general run_prolif uses inside, but you can run them directly so you don't need to rerun prolif calculations and can just change the pictures parameters by using run_prolif output csv files)

As for the other improvements, currently I am super busy with another project of mine, so some not-critical features might take longer to be implemented, but once I have more time I will return to it. Thanks for understanding!

prolif_draw_by_frame -h
usage: prolif_draw_by_frame [-h] -i [FILENAME ...] [-o FILENAME] [--occupancy float] [--filt_only_H] [--width int] [--height int] [--base_size int] [--point_size int]

Draw prolif plot for analysis of contacts by each frame of the unique ligand

options:
  -h, --help            show this help message and exit
  -i [FILENAME ...], --input [FILENAME ...]
                        input file with prolif output for the unique molecule. Supported formats: *.csv. Ex: plifs.csv
  -o FILENAME, --output FILENAME
                        output prefix name
  --occupancy float     minimum occupancy of the unique contacts to show. Show all contacts by default
  --filter_only_H         filter residues where only hydrophobic contacts occur
  --width int           width of the output picture
  --height int          height of the output picture
  --base_size int       base size of the output picture
  --point_size int      dots size of the output picture

prolif_drawmap -h
usage: prolif_drawmap [-h] -i FILENAME [FILENAME ...] [-o FILENAME] [--occupancy float] [--width int] [--height int] [--base_size int] [--point_size int]

Draw prolif plot for analysis binding mode of multiple ligands

options:
  -h, --help            show this help message and exit
  -i FILENAME [FILENAME ...], --input FILENAME [FILENAME ...]
                        input file with compound. Supported formats: *.csv. Ex: prolif_output.csv
  -o FILENAME, --output FILENAME
                        output prefix name
  --occupancy float     minimum occupancy of the unique contacts to show
  --width int           width of the output picture
  --height int          height of the output picture
  --base_size int       base size of the output picture
  --point_size int      dots size of the output picture

Hope it will help and if you need more details please let me know!