Hello,
I am doing MMPBSA.py calculation using Amber16 and AmberTools 16. Each time
I encountered the following error :
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using
/export/home/p170030cy/Amber16/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /export/home/p170030cy/Amber16/amber16/bin/cpptraj
Preparing trajectories for simulation...
51 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/export/home/p170030cy/Amber16/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
File "/export/home/p170030cy/Amber16/amber16/bin/MMPBSA.py", line 100, in
<module>
app.run_mmpbsa()
File
"/export/home/p170030cy/Amber16/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/export/home/p170030cy/Amber16/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/export/home/p170030cy/Amber16/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /export/home/p170030cy/Amber16/amber16/bin/mmpbsa_py_energy
failed with prmtop kcsa-tea-dry.parm7!
Exiting. All files have been retained.
And this is the last lines of _MMPBSA_complex_gb.mdout.0
VDWAALS = -nan EEL = -nan EGB = nan
1-4 VDW = 1535.5730 1-4 EEL = 14130.9250 RESTRAINT =
0.0000
ESURF = 0.0000
Processing frame 8
eff.c(2717) enb14 --> 1526.827
eff.c(2718) eel14 --> 14098.639
eff.c(2776) enb --> -nan
eff.c(2777) eel --> -nan
it stops here.
And the following is my input file:
&general
endframe=1000, keep_files=2, startframe=950,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100, inp=1, radiopt=0,
What could be the reason for this error and how one can solve it?
Thanks in Advance...
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Received on Thu Mar 07 2019 - 22:00:03 PST
