MMPBSA_error: Got error post installation success during test run

Cn rahul

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Mar 6, 2023, 9:53:42 PM3/6/23

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The installation was done in Centos 7. Kindly help with the following error

MMPBSA_error: /use/local/gromacs/bin/gmx make_ndx failed when querying index.ndx.

Except one test passed (comp_receptor) without error Rest 8 failed.

marioe911116

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Mar 6, 2023, 9:59:46 PM3/6/23

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which command line did you use? coudl you please send us some of the log files reporting the errors?

Cn rahul

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Mar 6, 2023, 10:07:59 PM3/6/23

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[INFO ] Starting gmx_MMPBSA v1.6.0
[INFO ] Command-line
mpirun -np 4 gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top -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 /root/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /root/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /root/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /root/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/local/gromacs/bin/gmx
[INFO ] Checking external programs...Done.

[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[ERROR ] MMPBSA_Error /usr/local/gromacs/bin/gmx make_ndx failed when querying index.ndx.
Check the gmx_MMPBSA.log file to report the problem.
File "/root/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 689, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 263, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(self.make_ndx), self.FILES.complex_index))
File "/root/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: /usr/local/gromacs/bin/gmx make_ndx failed when querying index.ndx
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

marioe911116

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Mar 6, 2023, 10:10:47 PM3/6/23

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are you susing GROMACS 2023?

Cn rahul

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Mar 6, 2023, 10:15:54 PM3/6/23

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Except comp_receptor passed the test. remaining failed.

gmxMMPBSA) [root@localhost guest]# gmx_MMPBSA_test
[INFO ] Cloning gmx_MMPBSA repository in /home/guest/gmx_MMPBSA_test
Cloning into '/home/guest/gmx_MMPBSA_test'...
remote: Enumerating objects: 21261, done.
remote: Counting objects: 100% (2093/2093), done.
remote: Compressing objects: 100% (446/446), done.
remote: Total 21261 (delta 1236), reused 2075 (delta 1229), pack-reused 19168
Receiving objects: 100% (21261/21261), 334.59 MiB | 3.99 MiB/s, done.
Resolving deltas: 100% (14789/14789), done.
[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
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Protein_ligand/ST/3.log)
[INFO ] Protein-Protein RUNNING
[ERROR ] Protein-Protein [ 2/ 9] ERROR
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Protein_protein/4.log)
[INFO ] Protein-DNA RUNNING
[ERROR ] Protein-DNA [ 3/ 9] ERROR
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Protein_DNA/5.log)
[INFO ] Protein-Glycan RUNNING
[ERROR ] Protein-Glycan [ 4/ 9] ERROR
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Protein_glycan/7.log)
[INFO ] Comp_receptor RUNNING
[INFO ] Comp_receptor [ 5/ 9] DONE
[INFO ] Alanine Scanning RUNNING
[ERROR ] Alanine Scanning [ 6/ 9] ERROR
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Alanine_scanning/12.log)
[INFO ] Stability calculation RUNNING
[ERROR ] Stability calculation [ 7/ 9] ERROR
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Stability/13.log)
[INFO ] Decomposition Analysis RUNNING
[ERROR ] Decomposition Analysis [ 8/ 9] ERROR
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Decomposition_analysis/14.log)
[INFO ] Interaction Entropy approximation RUNNING
[ERROR ] Interaction Entropy approximation [ 9/ 9] ERROR
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Entropy_calculations/Interaction_Entropy/15.log)
(gmxMMPBSA) [root@localhost guest]#

9.log

Cn rahul

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Mar 6, 2023, 10:16:46 PM3/6/23

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No gromacs 2018.8

Cn rahul

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Mar 6, 2023, 10:18:38 PM3/6/23

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I am using gromacs 2018.8 installed in root.

Mario Ernesto

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Mar 6, 2023, 10:18:48 PM3/6/23

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but this 9.log is finalized correctly, right? how about the log for those who didn't?

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Cn rahul

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Mar 6, 2023, 10:24:17 PM3/6/23

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Other logs gave the same error. I have attached the log for one below

[INFO ] Protein-Ligand (Single trajectory approximation) RUNNING
[ERROR ] Protein-Ligand (Single trajectory approximation) [ 1/ 9] ERROR
Please, check the test log
(/home/guest/gmx_MMPBSA_test/examples/Protein_ligand/ST/3.log)

3.log

Mario Ernesto

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Mar 6, 2023, 10:35:07 PM3/6/23

to Cn rahul, gmx_MMPBSA

could you please send the gmx_MMPBSA.log file that is located in the same folder?

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Cn rahul

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Mar 6, 2023, 10:47:20 PM3/6/23

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Please find the attachment of the gmx_MMPBSA.log below

gmx_MMPBSA.log

marioe911116

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Mar 6, 2023, 10:54:22 PM3/6/23

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The files for the test were created with GROMCAS 2022.3 and ist conflicting with your GROMACS 2018... We'll solve this asap... by you can use gmx_MMPBSA... seems to be working well for systems prepared with older GROMACS versions

Cn rahul

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Mar 7, 2023, 12:07:05 AM3/7/23

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Sir,

As suggested will go ahead with using the gmx_MMPBSA tool installed along with gromacs 2018.8.