Re: [AMBER] mmPBSA error in Amber19 suite

From: jacky zhao <>
Date: Sat, 17 Aug 2019 19:40:29 +0800

Hi everyone,
   I have recompiled the latest amber18 to test However, the similar error can be found. I have also used our previous MD trajectory to test the Previously, this MD trajectory can be calculated by amber18 without any problem.

  I am wondering why cpptraj could not reach the complex topology file. All these topology files were generated by

Anyone could give some suggestions?

Thank you a lot.



> 在 2019年8月16日,上午1:10,jacky zhao <> 写道:
> 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 -O -i -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/", line 100, in <module>
> app.run_mmpbsa()
> File "/home/mydata/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/", line 218, in run_mmpbsa
>, self.stdout)
> File "/home/mydata/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/", line 82, in run
>, stdout=stdout, stderr=stderr)
> File "/home/mydata/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/", 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

AMBER mailing list
Received on Sat Aug 17 2019 - 05:00:02 PDT
Custom Search