[AMBER] MMPBSA Quasi-Harmonic Entropy

From: Sachin Natesh <snatesh.uchicago.edu>
Date: Mon, 12 Dec 2016 22:16:26 -0600


I'm using the mmpbsa script in Ambertools16 to calculate the binding
affinity between a protein and membrane. The simulations were first run in
NAMD, and I used chamber in parmed with my *.psf and CHARMM
topology/parameter files to generate *.prmtop files. I have 400 snapshots,
saved every 240 ps.

While PB/GB calculations work, I'm having problems when trying to refine
these calculations with a quasi-harmonic approximation to the entropy. The
calculation fails on my unsolvated complex prmtop file, but there is no
data printed to the _MMPBSA_cpptraj_entropy.out file. Below is the error

Beginning quasi-harmonic calculations with /Users/sachin/amber16/bin/cpptraj

  File "/Users/sachin/amber16/bin/MMPBSA.py", line 100, in <module>


  File "/Users/sachin/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa

    self.calc_list.run(rank, self.stdout)

  File "/Users/sachin/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run

    calc.run(rank, stdout=stdout, stderr=stderr)

  File "/Users/sachin/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 375, in run

    Calculation.run(self, rank, stdout=self.output)

  File "/Users/sachin/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run


CalcError: /Users/sachin/amber16/bin/cpptraj failed with prmtop


Other relevant output/input files can be found here
link). I'd appreciate any insight that might help me resolve this issue.

Thanks and regards,

Sachin Natesh
AMBER mailing list
Received on Mon Dec 12 2016 - 20:30:02 PST
Custom Search