Hello again,
I tried to run the test cases with my files. For that, I just replaced
the top and inpcrd files with my corresponding files (and commented out
the dacdif part). For GB, it ran through again without issue. For PB, I
got the same error as before. So maybe there is something wrong with my
files? What part could let GB run but not PB?
An important note might be that I created the top files for MMPBSA AFTER
I had already done the simulation, and I only added the PBRadii option
then. Furthermore I use tip5p, but that should not be relevant for
implicit solvent calculations, right? Finally I am also loading custom
parameters for special residues, but this has also not been a problem
before.
Does any of this give you an idea of whats going on?
Thank you very much again!
Best regards,
Richard
On 4/5/22 20:42, Ray Luo wrote:
> Great! Could you next use an input file in one of the test cases that is
> closest to your own job without change and run your job again? Let's see
> what happens.
>
> 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 Tue, Apr 5, 2022 at 8:38 AM Richard Kullmann <
> Richard.Kullmann.mpikg.mpg.de> wrote:
>
>> Dear Ray,
>>
>> both GB and PB tests run without issues.
>>
>> Best,
>>
>> Richard
>>
>>
>> -------- Forwarded Message --------
>> Subject: Re: [AMBER] MMPBSA.py PB calculation not working
>> Date: Tue, 5 Apr 2022 07:48:50 -0700
>> From: Ray Luo <rluo.uci.edu>
>> To: Richard Kullmann <richard.kullmann.mpikg.mpg.de>
>>
>>
>>
>> Richard,
>>
>> Do you see any problem running mmpbsa.py tests under
>> $AMBERHOME/AmberTools/test/mmpbsa_py?
>>
>> 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 Tue, Apr 5, 2022 at 1:23 AM Richard Kullmann
>> <Richard.Kullmann.mpikg.mpg.de <mailto:Richard.Kullmann.mpikg.mpg.de>>
>> wrote:
>>
>> Hello Ray,
>>
>> I had actually tried that as well, and got exactly the same error
>> message...Considering that GB worked fine, I would also assume that
>> the
>> input prmtop and inpcrd files are fine. Is that correct?
>> Best regards,
>>
>> Richard
>>
>> On 4/4/22 17:33, Ray Luo 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
>> <mailto: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 <http://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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Received on Wed Apr 06 2022 - 03:00:02 PDT
