Hello to everyone!
So, I am trying to run MMPBSA.py.MPI for nmode and the calculation for
_MMPBSA_complex_nm.out gets stack in minimazition. The error I receive in
progress . log (between endless lines of Line minimizer aborted ...) is
Line minimizer aborted: max number of iterations reached
Line minimizer aborted: rounding error
Second derivatives are not supported for periodic systems; exiting.
File "/opt/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
app.run_mmpbsa()
File "/opt/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
Calculation.run(self, rank, stdout=self.output % rank)
File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
self.prmtop))
CalcError: /opt/amber14/bin/mmpbsa_py_nabnmode failed with prmtop Com.prmtop!
Error occured on rank 3.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
Line minimizer aborted: max number of iterations reached
I have try many different ways of setting up the process (such as: use
same protein but different ligands in amber12 & amber 14, gb=0 or 1, ways
of producing prmtops ... ) but always the same error. So, should I try
mm_pbsa instead? Has to do with the protein ? With the system ? Any other
ways for estimating entropy ?
Thank you in advance,
Sofia V.
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Received on Thu Apr 09 2015 - 08:00:05 PDT
