Entropy calculation Error

[gagandeep singh]

Hi everyone,

I am trying to calculate the binding free energy of my protein-ligand complex (Single trajecytory) and getting the following error during entropy calculation using NMODE:

Beginning nmode calculations with /home/gsk/anaconda3/envs/AmberTools20/bin/mmpbsa_py_nabnmode
  calculating complex contribution...
  File "/home/gsk/anaconda3/envs/AmberTools20/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 209, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 84, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 323, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 158, in run
    raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/gsk/anaconda3/envs/AmberTools20/bin/mmpbsa_py_nabnmode failed with prmtop COM.prmtop!
Exiting. All files have been retained.

Kindly help me to resolve the error.

Thanks and Regards

Gagandeep Singh

--

Assistant Research Officer (Biotechnology)

Central Ayurveda Research Institute, Jhansi

Ph.D. Scholar

KSBS, IIT Delhi

Mob- 8178163366, 8285477478

[Mario Ernesto]

HI there! send us the files you are using please, so we can check what's going wrong...

cheers!

Mario

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[marioe911116]

Just to sum up here as we talked about this online... 

check the *_nm.out files and if there is nothing wrong with them or no error has been printed, probably it is that you ran out of RAM... NMODE calculations require a considerable amount of RAM depending on the number of atoms in your system. The amount of total RAM consumed during the calculation will be: RAM for 1 frame * number of threads... It's recommended to perform some preliminary test on a few frames first and see how it works...