MMPBSA ERROR:

[Sridhar Kulkarni]

The mmpbsa gave the error that atoms in complex and topology are not matching what can i do to solve this error.

[INFO   ] Building Normal Complex Amber topology...
[ERROR  ] MMPBSA_Error

The number of atoms in the topology (6595) and the complex structure (6464) 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 558, in gmxtop2prmtop
    GMXMMPBSA_ERROR(f"The number of atoms 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 atoms in the topology (6595) and the complex structure (6464) 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.

[gmx_MMPBSA]

Please, attach the gmx_MMPBSA.log file

[Sridhar Kulkarni]

Here is the log file

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[Mario E. Valdes-Tresanco]

could you please send the files you are using?

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[Sridhar Kulkarni]

I have uploaded the required files in the folder.

https://drive.google.com/drive/folders/1_OIdWD7EOTIir4FAqkTgQamTz_g7V-J6?usp=sharing

[Mario E. Valdes-Tresanco]

for some reason in the index file the ligand UNL contains 29 atoms when it should be 26... please, create a brand new index file, use it as an index file for the calculations, and let me know if that solves the problem...

gmx make_ndx -f production_Extend_100ns.tpr -o index_mod.ndx

On Thu, Nov 23, 2023 at 10:44 PM Sridhar Kulkarni <sridha...@gmail.com> wrote:

I have uploaded the required files in the folder.

https://drive.google.com/drive/folders/1_OIdWD7EOTIir4FAqkTgQamTz_g7V-J6?usp=sharing

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[Sridhar Kulkarni]

That worked, Thank you so much.