Hi All,
I am trying to run MMPBSA.py, but I am getting a strange error regarding the box.
bash-4.1$ MMPBSA.py -O -i mmpbsa.in -y traj.mdcrd
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /home/jesorensen/Apps/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /home/jesorensen/Apps/amber12/bin/cpptraj
Preparing trajectories for simulation...
Error: Expect only 3 or 6 box coords, got 4
Error: Box line=[ 5.860 161.489 73.556 23.118
]
Error: Could not set up traj.mdcrd for reading.
Error: trajin: Could not set up trajectory.
I can process the trajectory just fine with good old ptraj, but cpptraj gives me the following error.
bash-4.1$ cpptraj -p solv_com.prmtop -y traj.mdcrd
CPPTRAJ: Trajectory Analysis. V13.1
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: []
Radius Set: modified Bondi radii (mbondi)
Warning: [solv_com.prmtop] ATOMIC_NUMBER not present in topology.
[traj.mdcrd] contains 2095 frames.
Warning: Box information present in parm but not in trajectory.
Warning: DISABLING BOX in parm [solv_com.prmtop]!
Any insight and workarounds are appreciated.
Best regards,
Jesper
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Received on Mon Jun 17 2013 - 21:00:02 PDT
