[AMBER] mmpbsa error

From: MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
Date: Fri, 17 Jul 2020 13:31:13 +0200

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


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Received on Fri Jul 17 2020 - 05:00:03 PDT
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