Re: [AMBER] MMPBSA.py PB calculation not working

From: Ray Luo <rluo.uci.edu>
Date: Fri, 8 Apr 2022 20:18:54 -0700

Hi All,

Richard and I have found the cause of the failure. My suggestion was to
turn on the sander option by setting "use_sander=1" in the input file. In
doing so, the mdout file has a lot more information for users to find out
what went wrong. It turns out one atom didn't have radius.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Mon, Apr 4, 2022 at 8:33 AM Ray Luo <rluo.uci.edu> wrote:
> Richard,
>
> How about you provide at least one option, such as "ipb=2," for the &pb
> section, as in the &gb section of the input?
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
>
> On Mon, Apr 4, 2022 at 3:02 AM Richard Kullmann <
> Richard.Kullmann.mpikg.mpg.de> wrote:
>
>> Hello,
>>
>> I am trying to run MMPBSA.py on my trajectories doing PB and GB
>> calculations. Here is the input file I used for trying out the script:
>>
>> Input file for running PB and GB
>> &general
>>     verbose=1,
>> /
>> &gb
>>    igb=2,
>> /
>> &pb
>> /
>>
>> When calling it with a command of the form
>>
>> MMPBSA.py -O -i mmpbsa.in -cp com.top -rp rec.top -lp lig.top -y
>> traj.crd  ,
>>
>> this is the final part of the output I get:
>>
>> Running calculations on normal system...
>>
>> Beginning GB calculations with
>> /cluster/apps/amber20/gnu/amber20_src/bin/mmpbsa_py_energy
>>    calculating complex contribution...
>>    calculating receptor contribution...
>>    calculating ligand contribution...
>>
>> Beginning PB calculations with
>> /cluster/apps/amber20/gnu/amber20_src/bin/mmpbsa_py_energy
>>    calculating complex contribution...
>>    File "/cluster/apps/amber20/gnu/amber20_src/bin/MMPBSA.py", line 100,
>> in <module>
>>      app.run_mmpbsa()
>>    File
>> "/cluster/apps/amber20/gnu/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py",
>>
>> line 218, in run_mmpbsa
>>      self.calc_list.run(rank, self.stdout)
>>    File
>> "/cluster/apps/amber20/gnu/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
>>
>> line 82, in run
>>      calc.run(rank, stdout=stdout, stderr=stderr)
>>    File
>> "/cluster/apps/amber20/gnu/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
>>
>> line 428, in run
>>      error_list = [s.strip() for s in out.split('\n')
>> TypeError: a bytes-like object is required, not 'str'
>> Exiting. All files have been retained.
>>
>> It seems that GB runs smoothly but PB doesn't.
>> Do you have any idea what could be the issue here?
>> Thank you very much in advance and best regards,
>>
>> Richard
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Fri Apr 08 2022 - 20:30:03 PDT
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