Hi Kshatresh!,
I tried your script, but the same error appears...:
Loading and checking parameter files for compatibility...
sander found! Using
/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/bin/sander
cpptraj found! Using
/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/bin/cpptraj
Preparing trajectories for simulation...
500 frames were processed by cpptraj for use in calculation.
Thanks so much in advance,
Myriam
Running calculations on normal system...
Beginning GB calculations with
/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/bin/sander
calculating complex contribution...
File
"/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/bin/MMPBSA.py", line 100, in
<module>
app.run_mmpbsa()
File
"/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in
run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in
run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in
run
self.prmtop))
CalcError:
/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/bin/sander failed with prmtop
smp-199mdk-dry.prmtop!
Exiting. All files have been retained.
Kshatresh Dutta Dubey <kshatresh.gmail.com> escribió:
> Hi Myriam,
>
> Give this a try:
> This is my script:
>
> Input file for running PB and GB
> &general
> startframe=1, endframe=5000, interval=10,verbose=2, keep_files=0,
> *use_sander=1,*
> /
> &gb
> igb=5, saltcon=0.150,
> /
> &decomp
> idecomp=3, dec_verbose=1,csv_format=0,
> print_res="1-137",
>
>
> On Fri, Jul 17, 2020 at 5:01 PM MYRIAN TORRES RICO <
> myriam.torres.iiq.csic.es> wrote:
>
>>
>> Hi everyone,
>>
>> I have a problem with the mmpbsa decomposition calculations. This
>> error appears:
>>
>>
>> Running calculations on normal system...
>>
>>
>> Beginning GB calculations with
>> /opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/
>> 5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/bin/sander
>> calculating complex contribution...
>> File
>> "/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/
>> 5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/bin/MMPBSA.py", line 100,
>> in
>> <module>
>> app.run_mmpbsa()
>> File
>> "/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/
>> 5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/lib/python2.7/site-packages/MMPBSA_mods/main.py",
>> line 218, in
>> run_mmpbsa
>> self.calc_list.run(rank, self.stdout)
>> File
>> "/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/
>> 5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
>> line 82, in
>> run
>> calc.run(rank, stdout=stdout, stderr=stderr)
>> File
>> "/opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/
>> 5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
>> line 157, in
>> run
>> self.prmtop))
>> CalcError:
>> /opt/cesga/easybuild-cesga/software/MPI/intel/2016.4.258/impi/
>> 5.1.3.223/amber/16-at-17-patchlevel-10-15-cuda/bin/sander failed with
>> prmtop
>> smp-199mdk-dry.prmtop!
>>
>>
>>
>> This is my script:
>>
>> Input file for running PB and GB
>> &general
>> startframe=1, endframe=5000, interval=10,verbose=2, keep_files=0,
>> /
>> &gb
>> igb=5, saltcon=0.150,
>> /
>> &decomp
>> idecomp=3, dec_verbose=1,csv_format=0,
>> print_res="1-137",
>>
>>
>>
>>
>> Any idea?
>>
>>
>> Thanks in advance!
>>
>>
>>
>> Myriam
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> With best regards
> ************************************************************************************************
> Dr. Kshatresh Dutta Dubey
> Department of Chemistry
> School of Natural Sciences
> Shiv Nadar University
> Gautam Budhha Nagar
> Uttar Pradesh-201314
> India
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jul 20 2020 - 01:00:03 PDT
