Hello all,
I am encountering an error with CPPTRAJ when setting “entropy=1” in the “&general” namelist.
The following is the error:
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/jat327/miniconda3/envs/AmberTools23/bin/cpptraj
mmpbsa_py_energy found! Using /home/jat327/miniconda3/envs/AmberTools23/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
120 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/jat327/miniconda3/envs/AmberTools23/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning quasi-harmonic calculations with /home/jat327/miniconda3/envs/AmberTools23/bin/cpptraj
terminate called after throwing an instance of 'std::bad_array_new_length'
what(): std::bad_array_new_length
File "/home/jat327/miniconda3/envs/AmberTools23/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/jat327/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/jat327/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/jat327/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 419, in run
Calculation.run(self, rank, stdout=self.output)
File "/home/jat327/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/jat327/miniconda3/envs/AmberTools23/bin/cpptraj failed with prmtop ArnC_tetramer.parm7!
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
srun: error: hal0287: task 0: Exited with exit code 1
The error is occurring in the “_MMPBSA_cpptrajentropy.in” file where it runs the following two lines:
matrix mwcovar name comp.matrix :1-1308
analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce
Is there a way around this “std::bad_array_new_length” error or should I compute the entropy contribution to the free energy separately say by using normal mode analysis?
Is there a way to run quasi-harmonic entropy calculations separately from the &general namelist?
Any information would be appreciated here.
Thank you!
Best,
Robert
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Received on Thu Mar 07 2024 - 07:00:02 PST
