It seems that the dummy file generated during MMPBSA running has problem
_MMPBSA_complex.pdb
_MMPBSA_receptor.pdb
_MMPBSA_ligand.pdb
If there are no problem in running MMPBSA, all three files have exactly complex pdb in _MMPBSA_complex.pdb , receptor pdb in _MMPBSA_receptor.pdb and ligand pdb in _MMPBSA_ligand.pdb
but in case of error, there are only receptor in all three pdb files
what kind of problem cause this error?
----- 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 - 23:00:02 PDT
