Hi,
There are two issues here. The std::bad_alloc error usually arises when
you’re out of memory or there is an integer overflow somewhere. It’s almost
impossible for me to tell which without knowing more details about your
system setup (machine you ran on, exact input, program versions, etc).
Second, 120 frames is nowhere near enough to properly populate a covariance
matrix of 1308 atoms, let alone residues. The general rule of thumb is you
should have at least the same number of frames as selected coordinates
(i.e. the number of selected atoms times 3), and ideally more. Also note
the entropy calculated from quasi-harmonic analysis is probably only going
to be useful if your system is in a single relatively well-behaved
conformation.
-Dan
On Thu, Mar 7, 2024 at 9:59 AM Robert Palmere via AMBER <amber.ambermd.org>
wrote:
> 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 Sun Mar 10 2024 - 09:30:02 PDT
