Hi everyone,
I have recompiled the latest amber18 to test MMPBSA.py.MPI. However, the similar error can be found. I have also used our previous MD trajectory to test the MMPBSA.py.MPI. 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 ante-MMPBSA.py.
Anyone could give some suggestions?
Thank you a lot.
Regards,
Lei
> 在 2019年8月16日，上午1:10，jacky zhao <jackyzhao010.gmail.com> 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 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 Sat Aug 17 2019 - 05:00:02 PDT
