[AMBER] mmPBSA error in Amber19 suite

From: jacky zhao <jackyzhao010.gmail.com>
Date: Fri, 16 Aug 2019 01:10:25 +0800

Hi everyone,
   I have used amber18 to calculate the binding affinity through mm/PBSA method without any problem. Recently, I have upgrade with the latest version of Amber19. The same script calculate the same trajectory, but the error occur. I have attached the script and the error information below:

mpirun --bind-to none -np 45 MMPBSA.py.MPI -O -i mmPBSA_composition.in -o HER2-Ab_wt_MMPBSA.dat -sp ../wt_wat.parm7 -cp ../HER2-Ab.parm7 -rp ../Ab.parm7 -lp ../HER2.parm7 -y ../../wt_wat_md_1ms.crd -eo ./HER2-Ab_wt_0-10000.csv

Beginning GB calculations with /home/mydata/opt/amber18/bin/sander
  calculating complex contribution...
  File "/home/mydata/opt/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
  File "/home/mydata/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/mydata/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/mydata/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 478, in run
CalcError: /home/mydata/opt/amber18/bin/cpptraj failed with prmtop ../HER2-Ab.parm7!
Error occured on rank 44.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 44

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Received on Thu Aug 15 2019 - 10:30:02 PDT
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