Hi Daniel
Yes I have production run files with .crd I don't know why it is coming though in my script I have mentioned
mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp PRMT7_WT_NH1.prmtop -cp complex.prmtop -rp receptor.prmtop -lp peptide.prmtop -y *.crd
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, July 8, 2016 9:09:46 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA
Are there any files in the directory with the '.mdcrd' extension? What
is the result of "ls *.mdcrd"?
-Dan
On Fri, Jul 8, 2016 at 12:42 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi
>
> now the errow that I am getting is
>
> TrajError: /nethome/axt651/apps/amber14/bin/cpptraj failed when querying *.mdcrd
>
>
> but I have not mentioned cpptraj anywhere in my script
>
>
> ________________________________
> From: Thakur, Abhishek <axt651.miami.edu>
> Sent: Friday, July 8, 2016 5:57:16 AM
> To: amber.ambermd.org
> Subject: [AMBER] MMPBSA
>
> Hi
>
> I am trying to do MMPBSA calculation using script
>
>
> mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp PRMT7_WT_NH1.prmtop -cp complex.prmtop -rp receptor.prmtop -lp peptide.prmtop -y *.crd
>
>
>
> But I am getting an error which I am unable to solve it
>
>
> Error: *.crd matches no files.
> File "/nethome/axt651/apps/amber14/bin/MMPBSA.py.MPI", line 103, in <module>
> app.file_setup()
> File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 156, in file_setup
> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 59, in make_trajectories
> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 467, in __init__
> self.Query()
> File "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 602, in Query
> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> TrajError: /nethome/axt651/apps/amber14/bin/cpptraj failed when querying *.crd
> Error occured on rank 0.
> Exiting. All files have been retained.
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
>
> I have cross checked MMPBSA.py.MPI is correctly installed in amber home directory
> Kindly help me out.
>
>
> thanking you,
> -AT
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
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Received on Fri Jul 08 2016 - 14:30:02 PDT
