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
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Received on Sat Jul 18 2020 - 03:30:03 PDT
