Re: [AMBER] MMPBSA - error

From: Ray Luo <rluo.uci.edu>
Date: Thu, 20 Apr 2017 09:06:20 -0700

Hi Anna,

It's really hard to know what's going on without further details.

Could you email me off the list an archive of the working folder?
Please use only 3 snapshots to make it small.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Thu, Apr 20, 2017 at 8:02 AM, Anna Cebrian Prats
<Anna.Cebrian.uab.cat> wrote:
> Hi amber users,
>
>
> I am trying to run a PB calculation, but I couldn't calculate the receptor contribution.
>
>
> The PB calculation began with the complex contribution and finished.
>
> However, when the receptor contribution starts appears this error :
>
>
> File "/opt/AMBER/amber16/bin/MMPBSA.py", line 100, in <module>
>
> app.run_mmpbsa()
>
> File "/opt/AMBER/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
>
> self.calc_list.run(rank, self.stdout)
>
> File "/opt/AMBER/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
>
> calc.run(rank, stdout=stdout, stderr=stderr)
>
> File "/opt/AMBER/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 431, in run
>
> self.prmtop) + '\n\t'.join(error_list) + '\n')
>
> CalcError: /opt/AMBER/amber16/bin/mmpbsa_py_energy failed with prmtop receptor.top!
>
>
> I already checked the receptor.top file and seems that everything is okay.
>
>
> How can deal with this error?
>
>
> Thank you in advanced
>
>
> Best,
>
>
> Anna
>
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Received on Thu Apr 20 2017 - 09:30:03 PDT