Interaction entropy

[Reza Khayat]

Hi,

I am running the following version of the program:

gmx_MMPBSA v1.5.2 based on MMPBSA version 16.0 and AmberTools 20

I receive the following error when trying to run gmx_MMPBSA_ana:

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/dialogs.py", line 585, in run_process
    obj = obj_method(**v['args']) if v['args'] else obj_method()
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/API.py", line 248, in load_file
    self._get_fromApp(self.fname)
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/API.py", line 830, in _get_fromApp
    app.parse_output_files(from_calc=False)
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1088, in parse_output_files
    self.get_iec2entropy(from_calc)
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1111, in get_iec2entropy
    self.calc_types.normal['ie'].parse_from_file(f'{self.pre}normal_interaction_entropy.dat',
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 241, in parse_from_file
    with open(filename) as of:
FileNotFoundError: [Errno 2] No such file or directory: '_GMXMMPBSA_normal_interaction_entropy.dat'
"""

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

Traceback (most recent call last):
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/dialogs.py", line 598, in run
    for result in imap_unordered_it:
  File "/home/rkhayat/anaconda3/envs/gmvMMPBSA/lib/python3.9/multiprocessing/pool.py", line 870, in next
    raise value
FileNotFoundError: [Errno 2] No such file or directory: '_GMXMMPBSA_normal_interaction_entropy.dat'
Abort (core dumped)

The initialisation file is attached. Any help would be appreciated. 

Best wishes,
Reza

[Mario Sergio Valdes]

Did you run the calculation with version 1.5.2 and open it with the same version gmx_MMPBSA_ana?
gmx_MMPBSA_ana v1.6.x is only compatible with versions higher than 1.5.5

[Reza Khayat]

I ran it with version 1.5.2 and tried opening it with version 1.5.6 (different computers).

[Mario Sergio Valdes]

Since we have made some major changes in certain versions, and we are only two people working on it, we have not been able to maintain a proper development cycle. We are working to improve this and achieve a final structure as a base to provide backward compatibility. At the moment, I am not sure if it will be compatible.
Anyway, you can send me the working directory (excludes input files like trajectories, tpr, etc.) zipped, and I'll try to give you a solution.
I'm sorry for the inconvenience.

[Reza Khayat]

Hi Mario,

Not a problem at all. I believe the file is too large to attach here. Please download from:

https://cuny907-my.sharepoint.com/:f:/g/personal/reza_khayat60_login_cuny_edu/EgpQAjojxH5DihTnBTi3dswB8bbqnmxsMfZenufnnvrStQ?e=tcEju0

Thanks for the help.

Best wishes,

[Mario Sergio Valdes]

Please, follow these steps to open your results with gmx_MMPBSA v1.6.1:

- open the _GMXMMPBSA_info file and localize the variable INPUT['gbsa'] = 2 (line 154)

- comment this line (add a # symbol in front or remove it) 

- run gmx_MMPBSA --rewrite-output in the working directory

These steps will regenerate the output files, recalculate the IE and generate a gmx_MMPBSA v1.6.1 compatible format.

Let me know if this works for you.