Hello,
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
message:
-----------------------------------------------
Beginning quasi-harmonic calculations with /Users/sachin/amber16/bin/cpptraj
File "/Users/sachin/amber16/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
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
self.prmtop))
CalcError: /Users/sachin/amber16/bin/cpptraj failed with prmtop
2M4J-single-finite-protein-membrane.prmtop!
--------------------------------------------
Other relevant output/input files can be found here
<
https://www.dropbox.com/sh/efkawxh1o7dmfnm/AADeYqaPuAiQbEPGiDr-79M-a?dl=0>
(dropbox
link). I'd appreciate any insight that might help me resolve this issue.
Thanks and regards,
Sachin Natesh
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Received on Mon Dec 12 2016 - 20:30:02 PST
