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Mario Sergio Valdes
Jan 21, 2023, 9:06:28 PM1/21/23
to gmx_MMPBSA
This problem seems to be a conda problem. Please check this thread (https://groups.google.com/g/gmx_mmpbsa/c/I5-lVPUcHts)
El sábado, 21 de enero de 2023 a las 20:06:11 UTC-5, bilal...@gmail.com escribió:
Can you help me to solve this error please ..
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Mario Sergio Valdes
Jan 23, 2023, 2:12:04 AM1/23/23
to gmx_MMPBSA
Finally, I found out what the problem is. The compilers installed (v1.5.2) version is incompatible with the wheel generation. The solution, at least for me is to install version v1.2.0.
conda install -c conda-forge compilers=1.2.0
conda install -c conda-forge compilers=1.2.0
I will update everything related to the documentation. Let me know if it worked for you.
Mario S.
El domingo, 22 de enero de 2023 a las 0:09:38 UTC-5, bilal...@gmail.com escribió:
it's always the same error ... unfortunately
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Mario Sergio Valdes
Jan 24, 2023, 11:08:19 PM1/24/23
to gmx_MMPBSA
No. Please, check the log file for each failed test and check what the error is
El martes, 24 de enero de 2023 a las 23:00:07 UTC-5, bouroug...@gmail.com escribió:
yes it's working..but when i run gmx_MPBSA_test, i get : (sir is this normal ?)[INFO ] Cloning gmx_MMPBSA repository...Done.[INFO ] Example STATE
--------------------------------------------------------------------------------
[INFO ] Protein-Ligand (Single trajectory approximation) RUNNING
[ERROR ] Protein-Ligand (Single trajectory approximation) [ 1/ 9] ERROR
[INFO ] Protein-Protein RUNNING
[ERROR ] Protein-Protein [ 2/ 9] ERROR
[INFO ] Protein-DNA RUNNING
[ERROR ] Protein-DNA [ 3/ 9] ERROR
[INFO ] Protein-Glycan RUNNING
[ERROR ] Protein-Glycan [ 4/ 9] ERROR
[INFO ] Comp_receptor RUNNING
[ERROR ] Comp_receptor [ 5/ 9] ERROR
[INFO ] Alanine Scanning RUNNING
[ERROR ] Alanine Scanning [ 6/ 9] ERROR
[INFO ] Stability calculation RUNNING
[ERROR ] Stability calculation [ 7/ 9] ERROR
[INFO ] Decomposition Analysis RUNNING
[ERROR ] Decomposition Analysis [ 8/ 9] ERROR
[INFO ] Interaction Entropy approximation RUNNING
[ERROR ] Interaction Entropy approximation [ 9/ 9] ERRORSir, is this normal?Thanks.
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Mario Sergio Valdes
Jan 24, 2023, 11:57:24 PM1/24/23
to gmx_MMPBSA
Sure, gladly. gmx_MMPBSA requires a working version of Gromacs, either in the PATH or in a custom path (see the gmx_path variable in this section https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/#miscellaneous-options). In your case, gmx_MMPBSA does not find any version of GROMACS on your machine. Make sure you have a version, preferably in the PATH, that is the same (preferably) or higher than the one you used to generate the trajectory.
El martes, 24 de enero de 2023 a las 23:43:23 UTC-5, bouroug...@gmail.com escribió:
Sir, can you explain how to solve this error[INFO ] Starting gmx_MMPBSA v1.5.7
[INFO ] Command-line
mpirun -np 4 gmx_MMPBSA MPI -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc -lm ligand.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/bbb/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/bbb/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/bbb/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/bbb/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version 4.x.x!
[ERROR ] MMPBSA_Error Could not find necessary program [ GROMACS ].
Check the gmx_MMPBSA.log file to report the problem.
File "/home/bbb/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/bbb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/bbb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 538, in make_prmtops
external_progs = utils.find_progs(self.INPUT, self.mpi_size) if self.master else {}
File "/home/bbb/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 740, in find_progs
GMXMMPBSA_ERROR('Could not find necessary program [ GROMACS ]')
File "/home/bbb/miniconda3/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.')
MMPBSA_Error: Could not find necessary program [ GROMACS ]
Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
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Mario Sergio Valdes
Jan 25, 2023, 12:20:59 AM1/25/23
to gmx_MMPBSA
gmx_MMPBSA searches for available executables both in the PATH and in the local folder. The algorithm checks if "gmx" is an executable in the above paths. Anyway, let's check several things to be sure:
- In your bashrc do you have the command line "source /usr/local/gromacs/bin/GMXRC" (or to the custom path if it is the case) or do you do it manually every time you use Gromacs?
- To which address do "which gmx" point?
- Is "gromacs" marked in red in the output of this command "echo $PATH| grep -i gromacs"?
- In your bashrc do you have the command line "source /usr/local/gromacs/bin/GMXRC" (or to the custom path if it is the case) or do you do it manually every time you use Gromacs?
- To which address do "which gmx" point?
- Is "gromacs" marked in red in the output of this command "echo $PATH| grep -i gromacs"?
El miércoles, 25 de enero de 2023 a las 0:08:16 UTC-5, bouroug...@gmail.com escribió:
Sir ...bbb@bbb-B150M-D2VX-SI:~/Desktop$ gmx --version
:-) GROMACS - gmx, 2022.4 (-:
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