Error while running gmx_MMPBSA

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Chardi Shahiya

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Feb 5, 2023, 5:06:10 AM2/5/23
to gmx_MMPBSA
File "/home/chardi/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/chardi/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/chardi/miniconda3/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 "/home/chardi/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/chardi/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 436, in gmx2pdb
    self.resi, self.resl, self.orderl = res2map(self.indexes, self.complex_str)
  File "/home/chardi/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 558, in res2map
    for e in value['num']:
TypeError: string indices must be integers
Exiting. All files have been retained.

Mario Sergio Valdes

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Feb 5, 2023, 12:53:34 PM2/5/23
to gmx_MMPBSA
Can you give us more information? We have no way to fix a bug if we cannot reproduce it. Please attach the file gmx_MMPBSA.log 
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