problem with mmpbsa problem

[Divpreet kaur]

Hi! I have been encountering this issue recently with the calculation. I have before hand removed pbc conditions and generated no pbc file for the execution of mmpbsa calculation but I am still getting this error.

I have attached the error message below for the reference.

 Please help me resolve this.

          Check the gmx_MMPBSA.log file to report the problem.
  File "/home/acbr/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/acbr/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.make_prmtops()
  File "/home/acbr/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 538, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/acbr/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/acbr/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 415, in gmx2pdb
    self.check4water()
  File "/home/acbr/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 437, in check4water
    GMXMMPBSA_ERROR(f'gmx_MMPBSA does not support water/ions molecules in any structure, but we found'
  File "/home/acbr/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: gmx_MMPBSA does not support water/ions molecules in any structure, but we found 17 molecules in the complex.
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

[Mario Ernesto]

Which version of gmx_MMPBSA are you using? Could you please share the gmx_MMPBSA.log file? 

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[marioe911116]

solved after defining the groups properly (without water molecules or ions) in the index for the receptor and ligand...

[Duangdao Wichadakul]

Hi, I still got the same error

"MMPBSA_Error gmx_MMPBSA does not support water/ions molecules in any structure, but we found 5 molecules in the complex.."

and not sure how to "defining the groups properly (without water molecules or ions) in the index for the receptor and ligand"

I tried using the data from

https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/examples/Entropy_calculations/Interaction_Entropy

and it worked!!.

I am using gmx_MMPBSA v1.5.6.

Please suggest.

Thanks!!.

--duangdao.

ในวันที่ วันจันทร์ที่ 4 กรกฎาคม ค.ศ. 2022 เวลา 8 นาฬิกา 18 นาที 22 วินาที UTC+7 marioe911116 เขียนว่า:

[Mario Sergio Valdes]

Please, try with the development version (python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.git -U)