Error during entropy calculations.

[gagandeep singh]

Hi Mario,

I am calculating the binding energy with entropic contribution for my 7 protein-ligand complexes. For 5 of the complexes it worked smoothly but for other two complexes i got the following error during entropy calculation:

1.

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 33, in <module>
    sys.exit(load_entry_point('gmx-MMPBSA==0+unknown', 'console_scripts', 'gmx_MMPBSA')())
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/app.py", line 100, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/main.py", line 212, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/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/gmx_MMPBSA-0+unknown-py3.9.egg/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/gmx_MMPBSA-0+unknown-py3.9.egg/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!

2.

Beginning nmode calculations with /home/gsk/anaconda3/envs/AmberTools20/bin/mmpbsa_py_nabnmode
  calculating complex contribution...
  calculating receptor contribution...
  File "/home/gsk/anaconda3/envs/AmberTools20/bin/gmx_MMPBSA", line 33, in <module>
    sys.exit(load_entry_point('gmx-MMPBSA==0+unknown', 'console_scripts', 'gmx_MMPBSA')())
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/app.py", line 100, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/main.py", line 212, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/gsk/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/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/gmx_MMPBSA-0+unknown-py3.9.egg/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/gmx_MMPBSA-0+unknown-py3.9.egg/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 REC.prmtop!

I would appreciate it if you can tell me how to troubleshoot here.

Thanks and Regards,

Gagandeep singh

--

Assistant Research Officer (Biotechnology)

Central Ayurveda Research Institute, Jhansi

Ph.D. Scholar

KSBS, IIT Delhi

Mob- 8178163366, 8285477478

[Mario Sergio Valdes]

Hi Gagandeep

It is difficult to know what happens here since the NMODE calculation fails in two different topologies

Could you send me these systems to review?

Mario S.

[Mario Sergio Valdes]

Hi Gangadeep, sorry for the delay, I've been doing tests to identify the problem. 

Everything seems to indicate that it is due to the saturation of the RAM. How many threads did you use and how much RAM do you have? Your system consumes about 5GB per thread, which means that it can completely consume RAM with just a few threads. Can you check if it is about this? After a lot of testing only that problem is the one that I have identified.

HTH!

Mario S.