running gmx_MMPBSA as non-root

[JORGE RICARDO QUINTERO SAUMETH]

Dear gmx_MMPBSA users,

Perhaps this may seem like a silly question. I have tried running gmx_MMPBSA as a non-root user and failed. I installed it in root mode and from that type of user everything works perfectly. However, when doing it with a non-root user with one of the examples that is in this distribution (test_files / Protein_ligand / MT) I get the following error:

============================================

::::quintero@quimica:~/gmx_MMPBSA-master/test_files/Protein_ligand/MT> gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc -rs rec.pdb -ri rec_index.ndx -rg 1 -rt rec_traj.pdb -lm ligand.mol2 -ls lig.pdb -li lig_index.ndx -lg 2 -lt lig_traj.pdb

[INFO   ] Started

[INFO   ] Loading and checking parameter files for compatibility...

[INFO   ] Checking external programs...

[INFO   ] cpptraj found! Using /opt/amber20/bin/cpptraj

[INFO   ] gmx_mpi found! Using /home/quintero/bin/GROMACS/bin/gmx_mpi

[INFO   ] tleap found! Using /opt/amber20/bin/tleap

[INFO   ] parmchk2 found! Using /opt/amber20/bin/parmchk2

[INFO   ] mmpbsa_py_energy found! Using /opt/amber20/bin/mmpbsa_py_energy

[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER Topologies from GROMACS files...

[INFO   ] Checking if supported force fields exists in Amber data...

[INFO   ] Get PDB files from structures files...

[INFO   ] Making gmx_MMPBSA index for complex...

  File "/usr/bin/gmx_MMPBSA", line 33, in <module>

    sys.exit(load_entry_point('gmx-MMPBSA==1.2.0', 'console_scripts', 'gmx_MMPBSA')())

  File "/usr/lib/python3.6/site-packages/gmx_MMPBSA-1.2.0-py3.6.egg/GMXMMPBSA/app.py", line 115, in gmxmmpbsa

    app.loadcheck_prmtops()

  File "/usr/lib/python3.6/site-packages/gmx_MMPBSA-1.2.0-py3.6.egg/GMXMMPBSA/main.py", line 591, in loadcheck_prmtops

    maketop = CheckMakeTop(FILES, INPUT, self.external_progs)

  File "/usr/lib/python3.6/site-packages/gmx_MMPBSA-1.2.0-py3.6.egg/GMXMMPBSA/make_top.py", line 100, in __init__

    self.getPDBfromTpr()

  File "/usr/lib/python3.6/site-packages/gmx_MMPBSA-1.2.0-py3.6.egg/GMXMMPBSA/make_top.py", line 135, in getPDBfromTpr

    c2 = subprocess.Popen(make_ndx_args, stdin=c1.stdout, stdout=self.log, stderr=self.log)

  File "/usr/lib64/python3.6/subprocess.py", line 729, in __init__

    restore_signals, start_new_session)

  File "/usr/lib64/python3.6/subprocess.py", line 1278, in _execute_child

    executable = os.fsencode(executable)

  File "/usr/lib64/python3.6/os.py", line 800, in fsencode

    filename = fspath(filename)  # Does type-checking of `filename`.

TypeError: expected str, bytes or os.PathLike object, not NoneType

Exiting. All files have been retained.

============================================

I appreciate all the help provided !!!!

Best regards

Jorge Quintero-Saumeth

[Mario Sergio Valdes]

Hi Jorge and Welcome!!!

There are no silly questions, we are here to help and learn. Feel free to ask any questions you have.

This is probably related to the Python environment it is running in. gmx_MMPBSA is based on MMPBSA.py and since it depends on its libraries, we decided to implement it in the AMBER miniconda environment as the original script is. We tested it by installing it in the AMBER miniconda environment and we had no problems. It also has the advantage of being isolated from the rest and therefore not be affected by updating the dependencies.

We recommend that you use the AMBER miniconda environment installed and tell us, if the error persists, we will gladly help you

[marioe911116]

we fixed a bug related to finding gromacs executable... please update the program:

(python executable) -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA --upgrade

and let us know how it goes...

[JORGE RICARDO QUINTERO SAUMETH]

Thank you very much for your support. In fact I was able to install your instructions and in fact I was able to do the first calculations using the GBBSA method. MY next step is to compare these results with those obtained with g_mmpsa. I have used the latter almost all the time. However, I want to analyze how its interface works.

We are in contact

[marioe911116]

That's awesome... please, let us know if possible your conclusions on the comparison between g_mmpbsa and our program. We have conducted some calculations and as a matter of fact, our program outperforms g_mmpbsa for a number of reasons, but it's always good to know if that's the case with other's people data and not just ours. Also, let us know if you need any further help...

support for calculations with charmm force filed is coming in few days... stay tuned :)

best!

[Martin Bonin]

I also used g_mmpbsa before and the results I got from gmx_MMPBSA were much more reasonable. But in my case this could also be caused by some atoms where g_mmpbsa could not recognize the atom type and set the radius to 1.

What I think is really useful in g_mmpbsa is the "energy2bfac" program, where the binding energy values from the decomposition analysis are stored in the b factor of a given pdb file. This helps a lot in visualizing the data to get a better overview. I wrote a small (a probably really bad) script for myself to do that with the gmx_MMPBSA results. I'll try to improve the script and if you are interested I can send it to you.

Best

Martin

[Mario Ernesto]

Thanks Martin for your feedback 😊... Actually the visualization of the energy decomposition in the b factor column of the pdb file is already implemented in our program. Check the decomposition tutorial and you will see how to save such pdb and visualize this information in three widely used visualization programs...

https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/test_files/Decomposition_analysis

                                  ***

Once the calculation is done, the GUI app (gmx_MMPBSA_gui) will show up. In this app, you can visualize the results for the GB calculation as well as the decomposition analysis. The results can be saved as *.csv file by clicking "File" in the upper left corner and then "Export GB/PB energy (csv)". Besides, a *.pdb file with per-residue energies in the b-factor column, can be saved by clicking "File" in the upper left corner and then "Energy to bfactor". This way, the contribution energy of every residue with its structure can be visualized in a molecular visualization program.

Follow these tutorials for coloring residues in a *.pdb file according to their contributions:

    PyMOL

    UCSF-Chimera

    VMD

                                     ***

Hope this helps! 

Best!

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[Martin Bonin]

Oh I was looking for that, but completely missed that. Since I run gmx_MMPBSA via a bash script for up to 90 simulations at once, I specify the output files via the output options (-o, -do, -eo, -deo) and automatically close the gui with an autoclicker (I tried -gui False, but that didn't work). So I was looking for a pdb output like -po or something similar.

[Mario Sergio Valdes]

Hi Martin.

I think we fixed the problem with the -gui option, although the way it is is not very elegant.  :(

We are thinking about changing the analysis tool name (gmx_MMPBSA_gui) to gmx_MMPBSA_ana. The current name may be confusing for some.

We believe that this tool, together with the portability of MMPBSA.py to GROMACS, is the main added value of gmx_MMPBSA. It is also the only one of its kind, so it has great potential. Currently, we are concentrating on the base support, that is, the correct operation of gmx_MMPBSA, as well as the support for a wide variety of systems (and the support for charmm force field, coming soon). We have plans to customize the graphics, internal fragments selection, the union, and comparison of graphics, change of the graphics type, etc. (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/projects/1# card-47547314)

Also, we are planning to create an API for this tool so that it allows working with it without having to open the graphical interface.

Additionally, I think we can add an option to process folders with multiple projects.

Best