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>
app.run_mmpbsa()
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
self.prmtop))
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
