Number of residues error

[sridha...@gmail.com]

As this error appeared I checked in the pdb file generated from complex It is showing that only 286 residuesar there, but why is it giving error? I have included all the relevent files in the google drive folder https://drive.google.com/drive/folders/1fV-JI-b3bRh8zUd6zOcN78AnF77RyGZd?usp=drive_link

The number of residues in the topology (286) and the complex structure (289) are different. Please check these files and verify that they are correct. Otherwise report the error...

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/bif-sssihl-12/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/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 562, in gmxtop2prmtop
    GMXMMPBSA_ERROR(f"The number of residues in the topology ({error_info[1]}) and the complex structure "
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:

The number of residues in the topology (286) and the complex structure (289) are different. Please check these files and verify that they are correct. Otherwise report the error...

Check the gmx_MMPBSA.log file to report the problem.

Exiting. All files have been retained.

Thank you.

[Sridhar Kulkarni]

The Error got solved after creating new index file . Thank you.

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