Dear amber users,
I am doing mmgbsa calculations on my protein-ligand systems using
ambertools 14 based on tutorial in amber web site.
------------------------------------------------------------------------------------
When I used follwing state, I obtained output file without any problem.
Input file for running GB without quasi-harmonic entropy calculation is as
follows:
&general
startframe=2000, endframe=4000, interval=5,
verbose=1, keep_files=1,
entropy=0,
/
&gb
igb=2, saltcon=0.100,
/
------------------------------------------------------------------------------------
But, When I used follwing state:
Input file for running GB with quasi-harmonic entropy calculation is as
follows:
&general
startframe=2000, endframe=4000, interval=5,
verbose=1, keep_files=1,
entropy=1,
/
&gb
igb=2, saltcon=0.100,
/
I encountered with following error:
Running calculations on normal system...
Beginning GB calculations with
/share/apps/amber/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
File "/share/apps/amber/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
app.run_mmpbsa()
File "/share/apps/amber/amber14/bin/MMPBSA_mods/main.py", line 218, in
run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line 79,
in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line
363, in run
Calculation.run(self, rank, stdout=self.output)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line
148, in run
self.prmtop))
CalcError: /share/apps/amber/amber14/bin/cpptraj failed with prmtop
comp.prmtop!
Error occured on rank 6.
Exiting. All files have been retained.
------------------------------------------------------------------------------------
In this condition, I decided to calculate entropy using nmode method.
But, When I used follwing state:
Input file for running entropy calculations using NMode is as follows:
&general
startframe=2000, endframe=4000, interval=5,
verbose=1, keep_files=1,
/
&nmode
nmstartframe=1, nmendframe=400, nminterval=4,
nmode_igb=1, nmode_istrng=0.1, maxcyc=1000, drms=0.01,
/
I encountered with following error:
Running calculations on normal system...
Beginning nmode calculations with
/share/apps/amber/amber14/bin/mmpbsa_py_nabnmode
calculating complex contribution...
Line minimizer aborted: step at upper bound 0.0069297972
File "/share/apps/amber/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
app.run_mmpbsa()
File "/share/apps/amber/amber14/bin/MMPBSA_mods/main.py", line 218, in
run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line 79,
in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line
309, in run
Calculation.run(self, rank, stdout=self.output % rank)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line
148, in run
self.prmtop))
CalcError: /share/apps/amber/amber14/bin/mmpbsa_py_nabnmode failed with
prmtop comp.prmtop!
Error occured on rank 6.
Exiting. All files have been retained.
------------------------------------------------------------------------------------
What means of Error occured on rank 6?
What are the resoans of these errors?
Is there problem in my comp.prmtop? If yes, why my first calculation (GB
without quasi-harmonic) was ok.
Any help will highly appreciated.
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Received on Tue Dec 01 2015 - 04:30:03 PST
