[AMBER] error in mdcrd box coordinates during MMPBSA calculation

From: JoAnne Babula <jbabula.umail.iu.edu>
Date: Thu, 11 Aug 2016 11:21:11 -0400


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>
  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__
  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
   startframe=20000, interval=80, endframe=120000, keep_files=2,
  igb=2, saltcon=0.100,
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 - 08:30:02 PDT
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