Sofia,
Line minimizer aborted: max number of iterations reached
I think this might be your primary issue. I'm assuming that the error
message means the same thing as it would in other programs, so in this case
it'd mean that MMPBSA is hitting the maximum number of times it can try to
use- reading through the manual, I'd venture to guess that maxcyc is the
value you'd want to look at increasing?
As a good way to double check, have you checked what the mdout file says?
Though, I've never seen this error before in relation to Amber, and have
very limited experience with nmode, so someone else might want to weigh in.
Best,
Kenneth
On Thu, Apr 9, 2015 at 10:39 AM, Sofia Vasilakaki <svasilak.chem.uoa.gr>
wrote:
> 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 - 08:30:05 PDT
