Error in a protein-membrane binding energy calculation

[DV]

Hello,

Thank you for your reply to my previous question. I wanted to ask another question about an error from a protein-membrane binding calculation. The GB calculations for the system finish properly but an error occurs when results are parsed to the output files:

-----------------------------------------

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /condapath/bin/sander
[INFO   ]   calculating complex contribution...
            100%|##########################################################################| 1/1 [elapsed: 11:06 remaining: 00:00]
[INFO   ]   calculating receptor contribution...
            100%|##########################################################################| 1/1 [elapsed: 00:06 remaining: 00:00]
[INFO   ]   calculating ligand contribution...
            100%|##########################################################################| 1/1 [elapsed: 11:06 remaining: 00:00]
[INFO   ] Parsing results to output files...

[ERROR  ] MMPBSA_Error 

Some energy terms are undefined. Please, check the input structure and trajectory. Check this section the docs for more info https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions

Check the gmx_MMPBSA.log file to report the problem.
  File "/condapath/myenv/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/condapath2/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
    app.parse_output_files()
  File "/condapath2/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 1215, in parse_output_files
    self.calc_types.normal[key]['complex'].parse_from_file(self.pre + basename[i] % 'complex',
  File "/condapath2/lib/python3.8/site-packages/GMXMMPBSA/amber_outputs.py", line 108, in parse_from_file
    AmberOutput._read(self)
  File "/condapath2/lib/python3.8/site-packages/GMXMMPBSA/amber_outputs.py", line 197, in _read
    self._get_energies(output_file)
  File "/condapath2/lib/python3.8/site-packages/GMXMMPBSA/amber_outputs.py", line 630, in _get_energies
    self['BOND'][self.frame_idx] = conv_float(words[2])
  File "/condapath2/lib/python3.8/site-packages/GMXMMPBSA/amber_outputs.py", line 603, in conv_float
    GMXMMPBSA_ERROR('Some energy terms are undefined. Please, check the input structure and trajectory. Check this '
  File "/condapath2/lib/python3.8/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:

Some energy terms are undefined. Please, check the input structure and trajectory. Check this section the docs for more info https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions

Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

----------------------------------------------------------------------

Do you know what could be causing the error? I assume that the problem is at least partially caused due to some failure in recognizing the phospholipid topologies (I am using a membrane of DOPC and DOPS) but do not know how to fix it.

Thank you for your time and help!

With best wishes,

[marioe911116]

the issue is indeed most commonly due to an improperly fitted trajectory, particularly for complex systems like protein-membrane simulations.

According to the official documentation and community reports:

"The structure defined in -cs, -rs, or -ls options is inconsistent, or the trajectory has not been fitted (remove PBC) properly. This is the most common error."
— gmx_MMPBSA Documentation​

This fitting problem leads to undefined energy terms because:

• Molecules might appear broken due to periodic boundary conditions (PBC).

• Internal distance calculations during MMPBSA get corrupted if parts of the complex drift or rotate inconsistently.

✅ Recommended Fix

Preprocess the trajectory as follows before using it in gmx_MMPBSA:

bash

CopyEdit

# 1. Remove PBC and center 

gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center -ur compact 

  # 2. Fit the trajectory to a reference (e.g., first frame) 

gmx trjconv -s md.tpr -f md_noPBC.xtc -o md_fit.xtc -fit rot+trans

Then, use md_fit.xtc with your gmx_MMPBSA command.

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So yes, lack of trajectory fitting is a well-documented and frequent cause of this issue, particularly when membrane systems are involved and accurate energy parsing is required.

Let me know if you’d like a one-liner command tailored to your input files.

Generated with gmx_MMPBSA-GPT (https://chatgpt.com/g/g-EQdUjhBwP-gmx-mmpbsa-gpt). Please contact the developers if you cannot solve the issue using this information.