Error in running nmode calculations

[Ketan Rohilla]

Hi there,

I am facing following error in entropy calculation:

[INFO   ] Beginning nmode calculations with /root/anaconda3/envs/gmxMMPBSA/bin/mmpbsa_py_nabnmode
[INFO   ]   calculating complex contribution...
Found an invalid periodicity in the prmtop file: 33
  File "/root/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 104, in gmxmmpbsa
    app.run_mmpbsa()
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 202, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 85, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 363, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 160, in run
    raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /root/anaconda3/envs/gmxMMPBSA/bin/mmpbsa_py_nabnmode failed with prmtop COM.prmtop!

[marioe911116]

something seems to be problematic in the periodicity... could you please send the files you are using to see if I can a way to solve this?...

make sure to include the topology as well as the associated itp files...

cheers! 

[Ketan Rohilla]

I want to know if we need to calculate the entropy to determine the binding free energy of the system? Because in your research article it is mentioned that, "When the entropic term is dismissed, the computed value is the effective free energy, which is usually sufficient for comparing relative binding free energies of related ligands".

I have already calculated Delta Total for my system. Is that can be termed as binding free energy or do we need to calculate entropy also?

Also, if yes then which method to use for entropy calculation and how to introduce that in our mmpbsa.in file? Can we calculate entropy separately without doing the whole calculation again?

Kindly help me out!

[Mario Ernesto]

I personally prefer to use mmpbgbsa method for relative binding free energies calculations... The method tends to overstimate grossly the "effective" (no entropy) or the binding free energy (with entropy )... you can try to calculate the interaction entropy (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Entropy_calculations/Interaction_Entropy/)

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[marioe911116]

if you are still interested in calculating the nmode entropy and you prepared your system with Amber force field (CHARMM force field is not allowed for nmode calculations), you can check this issue when we proposed a workaround for calculating the nmode entropy in systems with DIHEDRAL_PERIODICITY = 0

https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/211#issuecomment-1090728473

cheers!