search

Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
217 stars 64 forks source link

gmx_MMPBSA_test Errors #316

Closed wangshuai-simulation closed 1 year ago

wangshuai-simulation commented 1 year ago

I got some errors when i run gmx_MMPBSA_test (gmx_MMPBSA v1.5.7 based on MMPBSA version 16.0 and AmberTools 20) Here are the details:

COMMAND LINE: gmx_MMPBSA_test -f /home/tea_yiming/wangshuai/test-gmxmmpbsa -t 0 -n 10
[INFO   ] Cloning gmx_MMPBSA repository in /home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test
Cloning into '/home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test'...
remote: Enumerating objects: 19588, done.
remote: Counting objects: 100% (270/270), done.
remote: Compressing objects: 100% (118/118), done.
remote: Total 19588 (delta 111), reused 220 (delta 83), pack-reused 19318
Receiving objects: 100% (19588/19588), 325.47 MiB | 17.25 MiB/s, done.
Resolving deltas: 100% (13784/13784), done.
Checking out files: 100% (678/678), done.
[INFO   ] Cloning gmx_MMPBSA repository...Done.
[INFO   ]                           Example                                STATE
[INFO   ] Protein-Ligand (Single trajectory approximation)               RUNNING
[INFO   ] Protein-Ligand (Single trajectory approximation)       [ 1/16]    DONE
[INFO   ] Protein-Protein                                                RUNNING
[INFO   ] Protein-Protein                                        [ 2/16]    DONE
[INFO   ] Protein-DNA                                                    RUNNING
[INFO   ] Protein-DNA                                            [ 3/16]    DONE
[INFO   ] Protein-Membrane                                               RUNNING
[INFO   ] Protein-Membrane                                       [ 4/16]    DONE
[INFO   ] Protein-Glycan                                                 RUNNING
[INFO   ] Protein-Glycan                                         [ 5/16]    DONE
[INFO   ] Metalloprotein-Peptide                                         RUNNING
[INFO   ] Metalloprotein-Peptide                                 [ 6/16]    DONE
[INFO   ] Comp_receptor                                                  RUNNING
[INFO   ] Comp_receptor                                          [ 7/16]    DONE
[INFO   ] Protein-Ligand (CHARMM force field)                            RUNNING
[INFO   ] Protein-Ligand (CHARMM force field)                    [ 8/16]    DONE
[INFO   ] Protein-ligand complex in membrane with CHARMMff               RUNNING
[INFO   ] Protein-ligand complex in membrane with CHARMMff       [ 9/16]    DONE
[INFO   ] Alanine Scanning                                               RUNNING
[INFO   ] Alanine Scanning                                       [10/16]    DONE
[INFO   ] Stability calculation                                          RUNNING
[INFO   ] Stability calculation                                  [11/16]    DONE
[INFO   ] Decomposition Analysis                                         RUNNING
[INFO   ] Decomposition Analysis                                 [12/16]    DONE
[INFO   ] Interaction Entropy approximation                              RUNNING
**[ERROR  ] Interaction Entropy approximation                      [13/16]   ERROR**
Please, check the test log (/home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test/examples/Entropy_calculations/Interaction_Entropy/15.log)
[INFO   ] Protein-Ligand (Multiple trajectory approximation)             RUNNING
[INFO   ] Protein-Ligand (Multiple trajectory approximation)     [14/16]    DONE
[INFO   ] Entropy calculation using Normal Mode approximation            RUNNING
**[ERROR  ] Entropy calculation using Normal Mode approximation    [15/16]   ERROR**
Please, check the test log (/home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test/examples/Entropy_calculations/nmode/17.log)
[INFO   ] Calculations using 3D-RISM approximation                       RUNNING
**[ERROR  ] Calculations using 3D-RISM approximation               [16/16]   ERROR**
Please, check the test log (/home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test/examples/3D-RISM/18.log)

So i check the related log files. For [ERROR Interaction Entropy approximation] 15.log shows:

……
[INFO   ] Parsing results to output files...
[INFO   ] Beginning Interaction Entropy calculations...
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
    app.parse_output_files()
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1103, in parse_output_files
    self.get_iec2entropy(from_calc)
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1123, in get_iec2entropy
    ie = InteractionEntropyCalc(edata, self.INPUT)
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 676, in __init__
    self._calculate()
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 683, in _calculate
    exp_energy_int = np.array([], dtype=np.float)
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/numpy/__init__.py", line 284, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'float'
……

About this numpy attribute error, according to a message from, do i need to downgrade numpy version (current version is 1.24.0 got from conda list) ?

For [ERROR: Entropy calculation using Normal Mode approximation] 17.log shows:

……
[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 100, in gmxmmpbsa
    app.file_setup()
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 138, in file_setup
    lig_frames, self.numframes_nmode) = make_trajectories(INPUT, FILES, self.mpi_size,
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 228, in make_trajectories
    raise MMPBSA_Error('More processors than complex nmode frames!')
MMPBSA_Error: More processors than complex nmode frames!
……

For [ERROR: Calculations using 3D-RISM approximation] 18.log shows:

……
[INFO   ] Building AMBER topologies from GROMACS files... Done.
[INFO   ] Loading and checking parameter files for compatibility...
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 100, in gmxmmpbsa
    app.file_setup()
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 127, in file_setup
    create_inputs(INPUT, self.normal_system, self.pre)
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/createinput.py", line 229, in create_inputs
    rism_mdin = SanderRISMInput(INPUT)
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/createinput.py", line 262, in __init__
    self.mdin.change(self.parent_namelist[key], key, INPUT[self.name_map[key]])
  File "/home/tea_yiming/.local/lib/python3.9/site-packages/ParmEd-3.4.3-py3.9-linux-x86_64.egg/parmed/amber/mdin/mdin.py", line 316, in change
    raise InputError('Unknown namelist (%s)!' % namelist)
InputError: Unknown namelist (rism)!
……
wangshuai-simulation commented 1 year ago

Thanks a lot if anyone can help me !

Valdes-Tresanco-MS commented 1 year ago

Thank you for reporting this problem Currently, I am in Cuban, so I can't work on the project now. The first error is definitively related to the NumPy version. I will check it as soon as possible. The second error is a bug. It should work fine if you decrease the number of CPUs. However, I have to fix it as of January 11 when I have access to my work PC. The last error is related to the version of parmed. You need to update the version from my repository as follows:

python -m pip install @.*** -U

If you have difficulties, please check this issue https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/301

Mario S.

El mar, 27 dic 2022 a las 12:50, Shuai Wang @.***>) escribió:

Thanks a lot if anyone can help me !

— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/316#issuecomment-1366075453, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIXZF4VGVFU54MIAIPA4HXTWPMT7BANCNFSM6AAAAAATKS2ASA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

wangshuai-simulation commented 1 year ago

Thanks for your reply. I solve all my questions except the error related to the NumPy version. Waiting for your further check. Thanks a lot !

Valdes-Tresanco-MS commented 1 year ago

Please try with conda install numpy<=1.24

Let me know if works for you

El mié., 28 dic. 2022 1:01 a. m., Shuai Wang @.***> escribió:

Thanks for your reply. I solve all my questions except the error related to the NumPy version. Waiting for your further check. Thanks a lot !

— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/316#issuecomment-1366391455, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIXZF4RYJLOTLRJPFXM6MXLWPPJUHANCNFSM6AAAAAATKS2ASA . You are receiving this because you commented.Message ID: @.***>

wangshuai-simulation commented 1 year ago

I solve the problem related to the NumPy version by downgrading NumPy version:

conda install numpy==1.23.5

Here are the outputs of gmx_MMPBSA_test

(gmxMMPBSA) [tea_yiming@node04 wangshuai]$ gmx_MMPBSA_test -f /home/tea_yiming/wangshuai/test-gmxmmpbsa -t 0 -n 6
[INFO   ] Cloning gmx_MMPBSA repository in /home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test
Cloning into '/home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test'...
remote: Enumerating objects: 19588, done.
remote: Counting objects: 100% (270/270), done.
remote: Compressing objects: 100% (118/118), done.
remote: Total 19588 (delta 111), reused 220 (delta 83), pack-reused 19318
Receiving objects: 100% (19588/19588), 325.47 MiB | 321.00 KiB/s, done.
Resolving deltas: 100% (13784/13784), done.
Checking out files: 100% (678/678), done.
[INFO   ] Cloning gmx_MMPBSA repository...Done.
[INFO   ]                           Example                                STATE
--------------------------------------------------------------------------------
[INFO   ] Protein-Ligand (Single trajectory approximation)               RUNNING
[INFO   ] Protein-Ligand (Single trajectory approximation)       [ 1/16]    DONE
[INFO   ] Protein-Protein                                                RUNNING
[INFO   ] Protein-Protein                                        [ 2/16]    DONE
[INFO   ] Protein-DNA                                                    RUNNING
[INFO   ] Protein-DNA                                            [ 3/16]    DONE
[INFO   ] Protein-Membrane                                               RUNNING
[INFO   ] Protein-Membrane                                       [ 4/16]    DONE
[INFO   ] Protein-Glycan                                                 RUNNING
[INFO   ] Protein-Glycan                                         [ 5/16]    DONE
[INFO   ] Metalloprotein-Peptide                                         RUNNING
[INFO   ] Metalloprotein-Peptide                                 [ 6/16]    DONE
[INFO   ] Comp_receptor                                                  RUNNING
[INFO   ] Comp_receptor                                          [ 7/16]    DONE
[INFO   ] Protein-Ligand (CHARMM force field)                            RUNNING
[INFO   ] Protein-Ligand (CHARMM force field)                    [ 8/16]    DONE
[INFO   ] Protein-ligand complex in membrane with CHARMMff               RUNNING
[INFO   ] Protein-ligand complex in membrane with CHARMMff       [ 9/16]    DONE
[INFO   ] Alanine Scanning                                               RUNNING
[INFO   ] Alanine Scanning                                       [10/16]    DONE
[INFO   ] Stability calculation                                          RUNNING
[INFO   ] Stability calculation                                  [11/16]    DONE
[INFO   ] Decomposition Analysis                                         RUNNING
[INFO   ] Decomposition Analysis                                 [12/16]    DONE
[INFO   ] Interaction Entropy approximation                              RUNNING
[INFO   ] Interaction Entropy approximation                      [13/16]    DONE
[INFO   ] Protein-Ligand (Multiple trajectory approximation)             RUNNING
[INFO   ] Protein-Ligand (Multiple trajectory approximation)     [14/16]    DONE
[INFO   ] Entropy calculation using Normal Mode approximation            RUNNING
[INFO   ] Entropy calculation using Normal Mode approximation    [15/16]    DONE
[INFO   ] Calculations using 3D-RISM approximation                       RUNNING
[INFO   ] Calculations using 3D-RISM approximation               [16/16]    DONE
--------------------------------------------------------------------------------
[INFO   ] Opening gmx_MMPBSA_ana...
ERROR:root:MMPBSA_Error Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is installed.
Check the gmx_MMPBSA.log file to report the problem.
Traceback (most recent call last):
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA_ana", line 8, in <module>
    sys.exit(gmxmmpbsa_ana())
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 126, in gmxmmpbsa_ana
    GMXMMPBSA_ERROR('Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is '
  File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
GMXMMPBSA.exceptions.MMPBSA_Error: Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is installed
Check the gmx_MMPBSA.log file to report the problem.

The last error doesn't matter to me, as i don't need gmx_MMPBSA_ana. Anyway, Thanks a lot !

Valdes-Tresanco-MS commented 1 year ago

If you are computing in an HPC, this is expected since the HPC has the graphical driver disabled. If you are computing in a PC, please install pyqt5 o pyqt6 python -m pip install pyqt5 or python -m pip install pyqt6

We encourage you to use gmx_MMPBSA_ana for your analyses, as it makes analyzing the results much easier. If you want to add any new analysis or graph, you can suggest us and we will try to implement it in future versions. Mario S.

El mié, 28 dic 2022 a las 4:05, Shuai Wang @.***>) escribió:

I solve the problem related to the NumPy version by downgrading NumPy version:

conda install numpy==1.23.5

Here are the outputs of gmx_MMPBSA_test

(gmxMMPBSA) @.*** wangshuai]$ gmx_MMPBSA_test -f /home/tea_yiming/wangshuai/test-gmxmmpbsa -t 0 -n 6 [INFO ] Cloning gmx_MMPBSA repository in /home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test Cloning into '/home/tea_yiming/wangshuai/test-gmxmmpbsa/gmx_MMPBSA_test'... remote: Enumerating objects: 19588, done. remote: Counting objects: 100% (270/270), done. remote: Compressing objects: 100% (118/118), done. remote: Total 19588 (delta 111), reused 220 (delta 83), pack-reused 19318 Receiving objects: 100% (19588/19588), 325.47 MiB | 321.00 KiB/s, done. Resolving deltas: 100% (13784/13784), done. Checking out files: 100% (678/678), done. [INFO ] Cloning gmx_MMPBSA repository...Done. [INFO ] Example STATE

[INFO ] Protein-Ligand (Single trajectory approximation) RUNNING [INFO ] Protein-Ligand (Single trajectory approximation) [ 1/16] DONE [INFO ] Protein-Protein RUNNING [INFO ] Protein-Protein [ 2/16] DONE [INFO ] Protein-DNA RUNNING [INFO ] Protein-DNA [ 3/16] DONE [INFO ] Protein-Membrane RUNNING [INFO ] Protein-Membrane [ 4/16] DONE [INFO ] Protein-Glycan RUNNING [INFO ] Protein-Glycan [ 5/16] DONE [INFO ] Metalloprotein-Peptide RUNNING [INFO ] Metalloprotein-Peptide [ 6/16] DONE [INFO ] Comp_receptor RUNNING [INFO ] Comp_receptor [ 7/16] DONE [INFO ] Protein-Ligand (CHARMM force field) RUNNING [INFO ] Protein-Ligand (CHARMM force field) [ 8/16] DONE [INFO ] Protein-ligand complex in membrane with CHARMMff RUNNING [INFO ] Protein-ligand complex in membrane with CHARMMff [ 9/16] DONE [INFO ] Alanine Scanning RUNNING [INFO ] Alanine Scanning [10/16] DONE [INFO ] Stability calculation RUNNING [INFO ] Stability calculation [11/16] DONE [INFO ] Decomposition Analysis RUNNING [INFO ] Decomposition Analysis [12/16] DONE [INFO ] Interaction Entropy approximation RUNNING [INFO ] Interaction Entropy approximation [13/16] DONE [INFO ] Protein-Ligand (Multiple trajectory approximation) RUNNING [INFO ] Protein-Ligand (Multiple trajectory approximation) [14/16] DONE [INFO ] Entropy calculation using Normal Mode approximation RUNNING [INFO ] Entropy calculation using Normal Mode approximation [15/16] DONE [INFO ] Calculations using 3D-RISM approximation RUNNING [INFO ] Calculations using 3D-RISM approximation [16/16] DONE

[INFO ] Opening gmx_MMPBSA_ana... ERROR:root:MMPBSA_Error Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is installed. Check the gmx_MMPBSA.log file to report the problem. Traceback (most recent call last): File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA_ana", line 8, in sys.exit(gmxmmpbsa_ana()) File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 126, in gmxmmpbsa_ana GMXMMPBSA_ERROR('Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is ' File "/home/tea_yiming/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in init raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.') GMXMMPBSA.exceptions.MMPBSA_Error: Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is installed Check the gmx_MMPBSA.log file to report the problem.

The last error doesn't matter to me, as i don't need gmx_MMPBSA_ana. Anyway, Thanks a lot !

— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/316#issuecomment-1366487038, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIXZF4WBLZQIY75GECIBQQDWPP7HDANCNFSM6AAAAAATKS2ASA . You are receiving this because you commented.Message ID: @.***>

marioernestovaldes commented 1 year ago

Reopened as we need to update the Numpy version in the requirements file...