The out file produced in MMPBSA is
_MMPBSA_complex_gb.mdout.0 --> maybe produced by mmpbsa_by_energy
_MMPBSA_normal_traj_cpptraj.out --> maybe produced by cpptraj
and I could find several warnings in _MMPBSA_normal_traj_cpptraj.out
but I 'm not sure whether this kind of warning is the reason of error (cpptraj failed with prmtop ...)
What could be the problem associated with it?
----- Original Message -----
From: David A Case
To: 홍종희 , AMBER Mailing List
Sent: Fri , September 20, 2024 03:07 AM
Subject: Re: [AMBER] MMPBSA error : cpptraj failed with prmtop ../../prep/com.top
On Thu, Sep 19, 2024, 홍종희 via AMBER wrote:
>
>while I run MD simulation and calculation of free energy by MMPBSA with MD simulation trajectory
>
>I got the following error:
>
>20 frames were processed by cpptraj for use in calculation.
>
>Running calculations on normal system...
>
>Beginning GB calculations with /usr/local/amber22/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/usr/local/amber22/bin/MMPBSA.py", line 100, in
> app.run_mmpbsa()
> File "/usr/local/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/usr/local/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/usr/local/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 519, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
>CalcError: /usr/local/amber22/bin/cpptraj failed with prmtop ../../prep/com.top!
Error messages will be in the mdout files created by cpptraj. You need to
look in those files. Or just run cpptraj by hand, asking it to compute the
energy. It will probably tell you why things failed.
...good luck...dac
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Received on Thu Sep 19 2024 - 19:30:02 PDT
