are you able to read GRL_INO_nowat.mdcrd with cpptraj?
Hai
On Thu, Aug 11, 2016 at 11:21 AM, JoAnne Babula <jbabula.umail.iu.edu>
wrote:
> Hello,
>
> I am trying to run a free energy calculation using 3 trajectories with
> MMPBSA. I received this error with the mdcrd for the complex:
>
> Error: In GRL_INO_nowat.mdcrd, expect only 3 or 6 box coords, got 4
> Error: Box line=[ -17.791 15.073 -3.686 -19.485
> ]
> Error: Could not set up GRL_INO_nowat.mdcrd for reading.
> Error: Could not set up input trajectory 'GRL_INO_nowat.mdcrd'.
> File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py.MPI", line
> 103, in <module>
> app.file_setup()
> File "/N/soft/rhel6/amber/intel/mpi/14/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 "/N/soft/rhel6/amber/intel/mpi/14/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 "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> site-packages/MMPBSA_mods/make_trajs.py", line 467, in __init__
> self.Query()
> File "/N/soft/rhel6/amber/intel/mpi/14/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: /N/soft/rhel6/amber/intel/mpi/14/amber14/bin/cpptraj failed
> when
> querying GRL_INO_nowat.mdcrd
> Error occured on rank 0.
> Exiting. All files have been retained.
>
>
>
> Do you know why this may have happened? Here is my input:
> ###Input file for running PB and GB####
> cat <<eof > mmpbsa.in
> Input file for running PB and GB
> &general
> startframe=20000, interval=80, endframe=120000, keep_files=2,
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
> eof
> mpirun -n 4 MMPBSA.py.MPI -O -i mmpbsa.in -o pbsa_karst.dat -sp
> ../../../../../INO/sim1/PREP/GRL_INO_solvate.top -cp
> ../../../../../INO/sim1/PREP/GRL_INO_nowat.top -rp
> ../../../../../Native/sim_1/PREP/native_nowat.top -lp
> ../../PREP/LINO_nowat.top -y GRL_INO_nowat.mdcrd -yr native_nowat.mdcrd -yl
> LINO_nowat.mdcrd >progress
>
>
>
> Thank you so much.
>
> --
> Very Respectfully,
>
> JoAnne J Babula
> Ph.D. Candidate, IUSM, Dept. of Pharmacology
> U.S. Army, 1LT, MS
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Received on Thu Aug 11 2016 - 12:00:02 PDT
