Sander error when running a Charmm generated protein-membrane system

[David Visentin]

Greeting,

I've encountered an error when trying to run gmx_mmpbsa on a Charmm protein ligand membrane system using the command:

gmx_MMPBSA -O -i mmpbsa.in -cs step7_production.tpr -ci index.ndx -cg 1 13 -ct md_fit.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

The output error is: 

_________________________________________________________________________________________
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning PB calculations with /home/zeljko1/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
[ERROR  ] CalcError /home/zeljko1/miniconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
   
If you are using sander and PB calculation, check the *.mdout files to get the sander error
.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/zeljko1/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/zeljko1/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 104, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/zeljko1/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 202, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/zeljko1/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 85, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/zeljko1/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 479, in run
    GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
  File "/home/zeljko1/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.')
CalcError: /home/zeljko1/miniconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
   
If you are using sander and PB calculation, check the *.mdout files to get the sander error

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

.log file reports the same error as terminal, and the .mdout reports nothing. It just stops at:
-------------------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------
   3.  ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

Cpptraj Generated Restart
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0
_________________________________________________________________________________________

Regarding some of the similar problems I've seen on this group:
- I think i have correctly removed PBC from my file
- i have ambertools 21

Attached are all the files I thought might be of help. With an additional link for the larger file such as .xtc.

https://drive.google.com/drive/folders/1GPiKu4KCj4f0Cii6y6mYcCpLbn9fy-IG?usp=sharing

I'm sorry for the bother but at this point i have no idea how to make it work.

Any idea would be of great help.

Best regards,

David Visentin

[Mario Sergio Valdes]

Please, check this thread (https://groups.google.com/g/gmx_mmpbsa/c/AlqRb0DqW30/m/V0LdffX-AgAJ)

[David Visentin]

Thank you for the response,

I'll try it first thing tomorrow morning. 

Best regards,

David Visentin 

[David Visentin]

Dear Sir,

You were right i was running out of RAM.

Thank you for the help. 

Warm regards,

David