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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
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MMPBSA_Error: No info files found! #37

Closed julianaamorim closed 3 years ago

julianaamorim commented 3 years ago

Hi Mario, after the installation I followed with the command gmx_MMPBSA_test to test all the examples and I encountered the error below, however I cannot identify the error in the installation steps

(base) juliana@juliana-VB:~$ gmx_MMPBSA_test -f /home/juliana/Documents -t all -n 10 [INFO ] Cloning gmx_MMPBSA repository in /home/juliana/Documents/gmx_MMPBSA_test Cloning into '/home/juliana/Documents/gmx_MMPBSA_test'... remote: Enumerating objects: 5030, done. remote: Counting objects: 100% (383/383), done. remote: Compressing objects: 100% (152/152), done. remote: Total 5030 (delta 234), reused 336 (delta 212), pack-reused 4647 Receiving objects: 100% (5030/5030), 245.85 MiB | 1.74 MiB/s, done. Resolving deltas: 100% (3559/3559), done. Updating files: 100% (326/326), done. [INFO ] Cloning gmx_MMPBSA repository...Done. [WARNING] Using all processors [INFO ] Example STATE

[INFO ] Protein-Ligand (Single trajectory approximation) RUNNING [INFO ] Protein-Protein RUNNING [ERROR ] Protein-Ligand (Single trajectory approximation) [ 1/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_ligand/ST/prot_lig_st.log) [INFO ] Protein-DNA RUNNING [ERROR ] Protein-Protein [ 2/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_protein/prot_prot.log) [INFO ] Protein-Membrane RUNNING [ERROR ] Protein-DNA [ 3/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_DNA/prot_dna.log) [INFO ] Protein-Glycan RUNNING [ERROR ] Protein-Membrane [ 4/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_membrane/memb_prot.log) [INFO ] Metalloprotein-Peptide RUNNING [ERROR ] Protein-Glycan [ 5/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_glycan/prot_glycan.log) [INFO ] Protein-DNA-RNA-IONs-Ligand RUNNING [ERROR ] Metalloprotein-Peptide [ 6/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Metalloprotein_peptide/metalloprot_pep.log) [INFO ] Protein-Ligand (CHARMM force field) RUNNING [ERROR ] Protein-DNA-RNA-IONs-Ligand [ 7/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_DNA_RNA_Ion_ligand/prot_dna_rna_ions_lig.log) [INFO ] Protein-ligand complex in membrane with CHARMMff RUNNING [ERROR ] Protein-Ligand (CHARMM force field) [ 8/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_ligand_CHARMMff/prot_lig_charmm.log) [INFO ] Alanine Scanning RUNNING [ERROR ] Protein-ligand complex in membrane with CHARMMff [ 9/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_membrane_CHARMMff/memb_charmm.log) [INFO ] Stability calculation RUNNING [ERROR ] Alanine Scanning [10/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Alanine_scanning/ala_scan.log) [INFO ] Decomposition Analysis RUNNING [ERROR ] Stability calculation [11/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Stability/stability.log) [INFO ] Protein-Ligand (Multiple trajectory approximation) RUNNING [ERROR ] Decomposition Analysis [12/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Decomposition_analysis/decomp.log) [INFO ] Interaction Entropy approximation RUNNING [ERROR ] Protein-Ligand (Multiple trajectory approximation) [13/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Protein_ligand/MT/prot_lig_mt.log) [INFO ] Entropy calculation using Normal Mode approximation RUNNING [ERROR ] Interaction Entropy approximation [14/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Entropy_calculations/Interaction_Entropy/ie.log) [INFO ] Calculations using 3D-RISM approximation RUNNING [ERROR ] Entropy calculation using Normal Mode approximation [15/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/Entropy_calculations/nmode/nmode.log) [ERROR ] Calculations using 3D-RISM approximation [16/16] ERROR Please, check the test log (/home/juliana/Documents/gmx_MMPBSA_test/docs/examples/3D-RISM/3drism.log)

[INFO ] Opening gmx_MMPBSA_ana... 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/juliana/Downloads/AmberTools20/amber20/miniconda/bin/gmx_MMPBSA_ana", line 8, in sys.exit(gmxmmpbsa_ana()) File "/home/juliana/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 126, in gmxmmpbsa_ana ifiles = get_files(parser) File "/home/juliana/.local/lib/python3.8/site-packages/GMXMMPBSA/analyzer/utils.py", line 162, in get_files GMXMMPBSA_ERROR('No info files found!') File "/home/juliana/.local/lib/python3.8/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.

Valdes-Tresanco-MS commented 3 years ago

Hi @julianaamorim This error is expected as all tests did not finish successfully.

Can you send me the log files of the failed tests? This way I can identify the problems, which I assume are related to the installation since they all failed.

Mario S.

julianaamorim commented 3 years ago

Thank you very much Mario, here follows the .log file

gmx_MMPBSA_test.log

Valdes-Tresanco-MS commented 3 years ago

I mean the log files for each example. After showing that each example ends in error a reference to a log file appears, please send me those files.

julianaamorim commented 3 years ago

3drism.log ala_scan.log decomp.log prot_dna.log prot_dna_rna_ions_lig.log prot_glycan.log prot_lig_mt.log prot_lig_st.log prot_lig_charmm.log memb_prot.log stability.log

Valdes-Tresanco-MS commented 3 years ago

As you can see from the log files, the error is that there is no Gromacs executable in the PATH. Make sure you have Gromacs installed and accessible from the PATH Best! Mario S.

julianaamorim commented 3 years ago

Beginner's mistake, I will continue this way, thank you very much for the prompt reply...

great week

Valdes-Tresanco-MS commented 3 years ago

No problem, we will gladly guide and help you. I will close the issue, feel free to open other at any time or ask in the group. You can also consult the Q&A section of the documentation.

Best wishes Mario S.