regarding the gromacs versions of input files for gmx_MMPBSA.

[Shilpa Sharma]

I have a question regarding the input files for gmx_MMPBSA.

When I run the gmx_MMPBSA on on the output files from gromacs v5.1.5. it ran successfully. However it gave the error to run the files generated from gromacs 2021 or 2022. 

Is it not for higher versions?? 

[Mario Sergio Valdes]

Please specify the gmx_MMPBSA version, the gromacs version used for MD simulation, and the version used with gmx_MMPBSA (may be the same or not)

[Shilpa Sharma]

gmx_MMBSA version is gmx_MMPBSA v1.6.2 and gromacs is gmx v2022.4

[Mario Ernesto]

Could you please submit the gmx_MMPBSA.log file?

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[Shilpa Sharma]

PFA,

Pl. look into this, urgent help required

[Mario Ernesto]

could you please run the command and paste the output from the terminal here?

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[Shilpa Sharma]

gmx_MMPBSA -O -i mmpbsa.in -cs md1.tpr -ct md1_noPBC.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/ncd/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/ncd/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/ncd/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/ncd/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/ncd/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/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 Protein_UNL (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 Protein (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 UNL (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 "/home/ncd/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 555, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 843, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/ncd/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 299, in read
    raise GromacsError('Duplicate definition of molecule %s'
GromacsError: Duplicate definition of molecule UNL
Exiting. All files have been retained.

[Mario Ernesto]

haven't seen an error like this one before... could you please send the files you are using

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[Shilpa Sharma]

https://drive.google.com/drive/folders/1JoC-Y45pXTxXxAYUho9bCjpQoZ98LJyR?usp=drive_link

pl. find the files on this link and try to troubleshoot.

[Shilpa Sharma]

any solution????

[Mario Ernesto]

For that specific system that you sent, the PROPER DIHEDRAL ANGLES term in lig.itp is not supported. That being said if you delete this section (lines 286-430) in lig.itp everything should run smoothly. 

PS: deleting this section should not affect the final results as these terms cancel each other when using Single Trajectpry Protocol

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[Shilpa Sharma]

NOT WORKING...............

[Mario Ernesto]

gmx_MMPBSA.log file?

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[Mario Sergio Valdes]

Are you sure you are using the same system as you send us? I couldn't reproduce the error either, and the instructions of Mario E work fine for me.