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unable to execute after installation #46

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ssinhachem opened this issue Jun 12, 2021 · 13 comments
Closed

unable to execute after installation #46

ssinhachem opened this issue Jun 12, 2021 · 13 comments
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bug Something isn't working medium priority Medium priority to solve the issue
Milestone
gmx_MMPBSA v1.5.0

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@ssinhachem
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Describe the issue
Installed the program gmx_MMPBSA with amber.python and also installed other dependencies as mentioned in program website. All path is set as instructed.

A clear and concise description of what the issue is.

If you will report an error, please complete this form
Installing collected packages: seaborn, mpi4py, gmx-MMPBSA
WARNING: The scripts gmx_MMPBSA, gmx_MMPBSA_ana and gmx_MMPBSA_test are installed in '/home/ssinha/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed gmx-MMPBSA-1.4.3 mpi4py-3.0.3 seaborn-0.11.1

(base) ssinha@susi:~/Desktop$ gmx_MMPBSA
[INFO ] Starting
[INFO ] Command-line
gmx_MMPBSA

InputError: No input file was provided!
Enter gmx_MMPBSA --help for help
(base) ssinha@susi:/Desktop$ gmx_MMPBSA
gmx_MMPBSA gmx_MMPBSA_ana gmx_MMPBSA_test
(base) ssinha@susi:/Desktop$ gmx_MMPBSA
gmx_MMPBSA gmx_MMPBSA_ana gmx_MMPBSA_test
(base) ssinha@susi:~/Desktop$ gmx_MMPBSA_test
[INFO ] Cloning gmx_MMPBSA repository in gmx_MMPBSA_test
Cloning into 'gmx_MMPBSA_test'...
remote: Enumerating objects: 6224, done.
remote: Counting objects: 100% (1581/1581), done.
remote: Compressing objects: 100% (527/527), done.
remote: Total 6224 (delta 1068), reused 1381 (delta 910), pack-reused 4643
Receiving objects: 100% (6224/6224), 255.69 MiB | 7.44 MiB/s, done.
Resolving deltas: 100% (4390/4390), done.
Updating files: 100% (364/364), done.
[INFO ] Cloning gmx_MMPBSA repository...Done.
[INFO ] Example STATE

[INFO ] Protein-Ligand (Single trajectory approximation) RUNNING
[INFO ] Protein-Protein RUNNING
[INFO ] Protein-Ligand (Single trajectory approximation) [ 1/12] DONE
[INFO ] Protein-DNA RUNNING
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/ssinha/amber20/miniconda/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/ssinha/.local/lib/python3.8/site-packages/GMXMMPBSA/tester.py", line 29, in calculatestar
return run_process(*args)
File "/home/ssinha/.local/lib/python3.8/site-packages/GMXMMPBSA/tester.py", line 33, in run_process
os.chdir(system[0])
FileNotFoundError: [Errno 2] No such file or directory: 'gmx_MMPBSA_test/docs/examples/Protein_protein'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/ssinha/.local/bin/gmx_MMPBSA_test", line 8, in
sys.exit(gmxmmpbsa_test())
File "/home/ssinha/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 146, in gmxmmpbsa_test
run_test(parser)
File "/home/ssinha/.local/lib/python3.8/site-packages/GMXMMPBSA/tester.py", line 132, in run_test
for x in imap_unordered_it:
File "/home/ssinha/amber20/miniconda/lib/python3.8/multiprocessing/pool.py", line 868, in next
raise value
FileNotFoundError: [Errno 2] No such file or directory: 'gmx_MMPBSA_test/docs/examples/Protein_protein'
To Reproduce
Steps to reproduce the behavior:

  1. Which system type are you running? (Protein-Protein, Protein-Ligand, etc)
  2. The command-line are you using.

Plz help
@Valdes-Tresanco-MS Valdes-Tresanco-MS added bug Something isn't working medium priority Medium priority to solve the issue labels Jun 12, 2021
@Valdes-Tresanco-MS
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It is definitely a bug and is related to the definition of the examples folder path. The way to solve it without much effort is to define the path explicitly and absolutely, that is, you must define the full path (eg. gmx_MMPBSA_test -f /home/mario/). A relative path will end in an error similar to this (eg. gmx_MMPBSA_test -f [ . , ./Documents , not define any path, etc])
We will solve it in the next release. Thank you for reported it

@Valdes-Tresanco-MS Valdes-Tresanco-MS added this to the gmx_MMPBSA v1.5.0 milestone Jun 12, 2021
@ssinhachem
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ssinhachem commented Jun 16, 2021 via email

@Valdes-Tresanco-MS
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The error should not be related to the forcefields variable since this variable only applies when it comes to Amber's force fields. When the ff is CHARMM (any version), the generation of Amber's topologies is by conversion (You can check this information here).
Please attach the gmx_MMPBSA.log file or the Traceback shown in the terminal to be able to identify the error

@ssinhachem
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ssinhachem commented Jun 16, 2021 via email

@Valdes-Tresanco-MS
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Valdes-Tresanco-MS commented Jun 16, 2021 •
edited

No serial and not MPI? what do you mean?
gmx_MMPBSA is independent of GROMACS compilation. It works with MPI independently, which can significantly reduce computing time. You can see how to run it here.
Example: mpirun -np 8 gmx_MMPBSA MPI -O ...

It is difficult to know. Assuming that the 53765 atoms correspond to protein (the water molecules are not taken into account in the calculation since it is an implicit solvent, nor the ions) and using about 8 CPU it should take between 1-3 hours approximately (Considering that it is PB only if it is GB, it can take 3-5 times less. If you calculate nmodes, the calculation time can be greatly increased by 10x or more)

Cheers
Mario S

@ssinhachem
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ssinhachem commented Jun 16, 2021 via email

@Valdes-Tresanco-MS
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Did you define the interaction_entropy = 1 or entropy = 2 (deprecated) variable?
The ΔG binding is calculated only if some entropy term was defined.
You can modify the _GMXMMPBSA_info file (only the interaction_entropy variable) to calculate it with gmx_MMPBSA_ana without run the calculation again

If you only calculate the ΔG effective, this term is named DELTA TOTAL and correspond to the ΔH value

HTH!
Mario S.

@ssinhachem
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ssinhachem commented Jun 16, 2021 via email

@Valdes-Tresanco-MS
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Note that the representation, as the value of the Interaction entropy contribution can vary with the number of frames. For more information, consult the documentation, where you can find related articles.
As the initial issue was solved, I will close it. Feel free to open another one if necessary. Also, consult our group.

Best regards
Mario S.

@Valdes-Tresanco-MS
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Sorry, I completely forgot that the issue was related to gmx_MMPBSA_test.

To better track other types of bugs, please open a new issue.

@ssinhachem
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ssinhachem commented Jun 16, 2021 via email

@ssinhachem
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ssinhachem commented Jun 16, 2021 via email

@marioernestovaldes
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Hello there! there are few things that I would like to point out about your results.

1- first thing first, gmx_MMPBSA works (which means it can process your files and give you a result). Now it's time to see what could be going wrong
2- I see you are using PB with inp=2 with gives you a high positive energy value for the desolvation. We have observed this before. You might want to check this section
3- It is recommended to use restraints when using the Interaction Entropy method since a large variation in the internal energy can give you high entropy values. See this paper

hope this helps!

Mario E

@Valdes-Tresanco-MS Valdes-Tresanco-MS mentioned this issue Jan 17, 2022
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@Valdes-Tresanco-MS Valdes-Tresanco-MS mentioned this issue Jan 28, 2022
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