gmxmmpbsa valueerror: too many values to unpack (expected 2) #437

mohammedGamila · 2023-11-29T20:12:15Z

mohammedGamila
Nov 29, 2023

hello,
i am processing a gmxmmpbsa on a protein-ligand complex and unfor. it keeps showing this message valueerror: too many values to unpack (expected 2), and tehe sequence runs as follows:
[INFO ] Starting gmx_MMPBSA v1.5.7
[INFO ] Command-line
mpirun -np 1 gmx_MMPBSA MPI -O -i mmpbsa.in -cs MD.tpr -ci new_index.ndx -cg 1 13 -ct MDnoPBC.xtc -cp topol2.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.

[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /share/apps/conda_envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /share/apps/conda_envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /share/apps/conda_envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /share/apps/conda_envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /eb/software/GROMACS/2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2/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...
[INFO ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal Ligand: Saving group 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Checking the structures consistency...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
File "/share/apps/conda_envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in
sys.exit(gmxmmpbsa())
File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
tops = self.gmxtop2prmtop()
File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 478, in gmxtop2prmtop
com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 765, in cleantop
rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in init
self.read(fname, defines, parametrize)
File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 357, in read
name, num = line.split()
ValueError: too many values to unpack (expected 2)
Exiting. All files have been retained.

please i need to know how to fix it

Answered by marioernestovaldes

Nov 30, 2023

in the [ molecules ] section it has:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 1SOL             16315
SOL         16239
NA               33
CL               43

Try deleting the additional SOL 16315 besides LIG 1 and see if that solves the issue

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 1
SOL         16239
NA               33
CL               43

View full answer

marioernestovaldes · 2023-11-30T00:00:30Z

marioernestovaldes
Nov 30, 2023
Collaborator

Seems something is wrong with the topology format, usually is one additional space that is ok for GROMACS but not ParmEd. could you please share the files you are using?

0 replies

mohammedGamila · 2023-11-30T08:16:35Z

mohammedGamila
Nov 30, 2023
Author

thanks alot for your help
here i upload my topol file
again i appreciate your effort
topol.zip

0 replies

marioernestovaldes · 2023-11-30T12:00:10Z

marioernestovaldes
Nov 30, 2023
Collaborator

in the [ molecules ] section it has:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 1SOL             16315
SOL         16239
NA               33
CL               43

Try deleting the additional SOL 16315 besides LIG 1 and see if that solves the issue

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 1
SOL         16239
NA               33
CL               43

1 reply

mohammedGamila Nov 30, 2023
Author

greetingd Dr.
this suggestion successfully solved the issue, but i have another issue the process works perfectly in the manual mode but always gives error in the sbatch mode which is:

ValueError: could not convert string to float: ''
Exiting. All files have been retained.

Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[55616,1],8]
Exit code: 1

please could you help me in this issue

marioernestovaldes · 2023-11-30T20:21:29Z

marioernestovaldes
Nov 30, 2023
Collaborator

I presume you are using an action.to Petron the calculations with sbatch and think this is generating the issue and not gmx_MMPBSA itself. Could you please comment on this?

1 reply

mohammedGamila Dec 1, 2023
Author

here i upload the sbatch file which contains only the code
run_mmgbsa.zip

marioernestovaldes · 2023-12-01T06:47:44Z

marioernestovaldes
Dec 1, 2023
Collaborator

Have you tried to run this command on your computer?

1 reply

mohammedGamila Dec 1, 2023
Author

the command works perfect but in sbatch gives me errors like i mentioned before

marioernestovaldes · 2023-12-01T06:56:15Z

marioernestovaldes
Dec 1, 2023
Collaborator

then, that is something related to the script or batch system and it has nothing to do with gmx_MMPBSA... try using the fewer possible flags in the sbatch script and see how it goes... then start incorporating others until you reach the error

1 reply

mohammedGamila Dec 1, 2023
Author

now it gives me this error
MMPBSA_Error: /eb/software/GROMACS/2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2/bin/gmx trjconv failed when querying MDnoPBC.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[ERROR ] MMPBSA_Error /eb/software/GROMACS/2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2/bin/gmx trjconv failed when querying MDnoPBC.xtc.
Check the gmx_MMPBSA.log file to report the problem.

marioernestovaldes · 2023-12-02T06:50:19Z

marioernestovaldes
Dec 2, 2023
Collaborator

can you attach the gmx_MMPBSA.log file?

1 reply

mohammedGamila Dec 2, 2023
Author

thanks for your help
i really appreciate it

gmx_MMPBSA.log

marioernestovaldes · 2023-12-02T09:31:04Z

marioernestovaldes
Dec 2, 2023
Collaborator

Seems.there is a missmatch between your index and your input structure and trajectory. Plese create a new index using the input structure.

If that doesn't solve the problem feel free to send us the files to see what's wrong

2 replies

mohammedGamila Dec 2, 2023
Author

thanks dr. mario
here i attach the files
New folder (3).zip
except the MDnoPBC.xtc file which exceeds 2 GB

mohammedGamila Dec 2, 2023
Author

dear mario
i removed the mpirun part and it worked fine

thank you for your patience and help

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

gmxmmpbsa valueerror: too many values to unpack (expected 2) #437

{{title}}

Replies: 8 comments 7 replies

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

Select a reply

gmxmmpbsa valueerror: too many values to unpack (expected 2) #437

mohammedGamila Nov 29, 2023

Replies: 8 comments · 7 replies

marioernestovaldes Nov 30, 2023 Collaborator

mohammedGamila Nov 30, 2023 Author

marioernestovaldes Nov 30, 2023 Collaborator

mohammedGamila Nov 30, 2023 Author

ValueError: could not convert string to float: '' Exiting. All files have been retained.

Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted.

Process name: [[55616,1],8] Exit code: 1

marioernestovaldes Nov 30, 2023 Collaborator

mohammedGamila Dec 1, 2023 Author

marioernestovaldes Dec 1, 2023 Collaborator

mohammedGamila Dec 1, 2023 Author

marioernestovaldes Dec 1, 2023 Collaborator

mohammedGamila Dec 1, 2023 Author

marioernestovaldes Dec 2, 2023 Collaborator

mohammedGamila Dec 2, 2023 Author

marioernestovaldes Dec 2, 2023 Collaborator

mohammedGamila Dec 2, 2023 Author

mohammedGamila Dec 2, 2023 Author

mohammedGamila
Nov 29, 2023

Replies: 8 comments 7 replies

marioernestovaldes
Nov 30, 2023
Collaborator

mohammedGamila
Nov 30, 2023
Author

marioernestovaldes
Nov 30, 2023
Collaborator

mohammedGamila Nov 30, 2023
Author

ValueError: could not convert string to float: ''
Exiting. All files have been retained.

Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.

Process name: [[55616,1],8]
Exit code: 1

marioernestovaldes
Nov 30, 2023
Collaborator

mohammedGamila Dec 1, 2023
Author

marioernestovaldes
Dec 1, 2023
Collaborator

mohammedGamila Dec 1, 2023
Author

marioernestovaldes
Dec 1, 2023
Collaborator

mohammedGamila Dec 1, 2023
Author

marioernestovaldes
Dec 2, 2023
Collaborator

mohammedGamila Dec 2, 2023
Author

marioernestovaldes
Dec 2, 2023
Collaborator

mohammedGamila Dec 2, 2023
Author

mohammedGamila Dec 2, 2023
Author