Valdes-Tresanco-MS
commented
2 years ago Can you check that the _GMXMMPBSA_info file is in the run folder? If so, can you run gmx_MMPBSA_ana -f _GMXMMPBSA_info?
Closed hima111997 closed 2 years ago
Valdes-Tresanco-MS
commented
2 years ago Can you check that the _GMXMMPBSA_info file is in the run folder? If so, can you run gmx_MMPBSA_ana -f _GMXMMPBSA_info?
hima111997
commented
2 years ago no it is not in the folder
Valdes-Tresanco-MS
commented
2 years ago Since gmx_MMPBSA finished fine, I would expect the _GMXMMPBSA_info file to be in the folder. I am not sure if it has something to do with that module error that is shown, because I have never seen this case. It seems that your environment has conflicts. Could you try following these installation instructions if you get the same error?
hima111997
commented
2 years ago i removed Ambertools21 and installed it using anaconda by following the instructions in the link you provided. then ran an analysis but the same error appeared:
WARNING:root:_GMXMMPBSA_info not found
ERROR:root:MMPBSA_Error No info files found!.
Check the gmx_MMPBSA.log file to report the problem.
Traceback (most recent call last):
File "/home/ibrahim/anaconda3/envs/AmberTools21/bin/gmx_MMPBSA_ana", line 8, in
the input file i used is this:
&general startframe=1, endframe=3,interval=1,temperature=310, verbose=1, keep_files=0, strip_mask=":WAT:CLA:SOD" / &gb igb=5, saltcon=0.154 / &decomp idecomp=2, dec_verbose=2, csv_format=1, print_res="within 10" /
maybe should i change the verbose value? since the file contains _ at the start and end of the file name?
Valdes-Tresanco-MS
commented
2 years ago maybe should i change the verbose value? since the file contains _ at the start and end of the file name?
The verbose variable only determines which term will be displayed in the output files. Unfortunately, I can't reproduce this error.
Are you running one of our examples or is it your system? If it's your system, consider sending us your files so we can check if it's a gmx_MMPBSA error
Mario S.
hima111997
commented
2 years ago I tried one of examples and it opened correctly. i noticed that the number of files produced from the example is larger than my data and the .in file of the example does not contain keep_files=0 which is found in my case. so i removed this argument and it opened well. So the solution is not to write keep_files = 0 or 1 in the input file. it must be 2 for gmx_MMPBSA_ana to work
hima111997
commented
2 years ago now i have another problem which is that when i try to open pymol by pressing the V checkbox it says that pymol is not in path. however i downloaded python from their website using the linux tar.bz archive as the installation command produced conflicts and made and alias to run it
Valdes-Tresanco-MS
commented
2 years ago I tried one of examples and it opened correctly. i noticed that the number of files produced from the example is larger than my data and the .in file of the example does not contain keep_files=0 which is found in my case. so i removed this argument and it opened well. So the solution is not to write keep_files = 0 or 1 in the input file. it must be 2 for gmx_MMPBSA_ana to work
The keep_files variable cannot be modified, so it is not defined in the documentation. I didn't even notice it in your input file. Since gmx_MMPBSA_ana use all data explicitly, it requires all files to be in the working directory. To avoid the huge number of files that are generated, we are working on implementing a single file, but it is still in the experimental phase.
now i have another problem which is that when i try to open pymol by pressing the V checkbox it says that pymol is not in path. however i downloaded python from their website using the linux tar.bz archive as the installation command produced conflicts and made and alias to run it
This happens because aliases are not executables, but command lines. To redefine an executable in the PATH, simply add the program bin folder or create a symbolic link of the executable
hima111997
commented
2 years ago thank you. i added it to the path and it is now working well
Bug summary
gmx_MMPBSA_ana does not open after finishing calculations.
The command used is: gmx_MMPBSA -O -i new_pbs.in -cs str_noLP.pdb -cp topol.top -ci index_LPH.ndx -cg 1 18 -ct step5_production_noPBC_noLP.xtc
Terminal output
Actual outcome
[INFO ] Opening gmx_MMPBSA_ana to analyze results...
Error processing line 1 of /home/ibrahim/Downloads/amb/miniconda/lib/python3.9/site-packages/distutils-precedence.pth:
Traceback (most recent call last): File "/home/ibrahim/Downloads/amb/miniconda/lib/python3.9/site.py", line 169, in addpackage exec(line) File "", line 1, in
ModuleNotFoundError: No module named '_distutils_hack'
Remainder of file ignored WARNING:root:_GMXMMPBSA_info not found ERROR:root:MMPBSA_Error No info files found!. Check the gmx_MMPBSA.log file to report the problem. Traceback (most recent call last): File "/home/ibrahim/Downloads/amb/miniconda/bin/gmx_MMPBSA_ana", line 8, in
sys.exit(gmxmmpbsa_ana())
File "/home/ibrahim/Downloads/amb/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 126, in gmxmmpbsa_ana
ifiles = get_files(parser)
File "/home/ibrahim/Downloads/amb/miniconda/lib/python3.9/site-packages/GMXMMPBSA/analyzer/utils.py", line 162, in get_files
GMXMMPBSA_ERROR('No info files found!')
File "/home/ibrahim/Downloads/amb/miniconda/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in init
raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')
GMXMMPBSA.exceptions.MMPBSA_Error: No info files found!. Check the gmx_MMPBSA.log file to report the problem.
[ERROR ] Unable to start gmx_MMPBSA_ana...
[INFO ] Finalized...
Expected outcome
gmx_MMPBSA_ana runs correctly
Additional information
these are the input parameters: &general startframe=1,interval=1, endframe=3, temperature=310, solvated_trajectory=0, verbose=1, keep_files=0, strip_mask=":WAT:CLA:SOD" / &gb igb=5, saltcon=0.154 / &decomp idecomp=2, dec_verbose=2, csv_format=1, print_res="within 10" /
Operating system
i am using ubuntu 20.04
gmx_MMPBSA_ana Version
gmx_MMPBSA_ana v1.4.3 based on MMPBSA version 16.0
Python version
Python 3.9.10
Installation
AmberTools compilation + pip