Loading and checking parameter files for compatibility... mmpbsa_py_energy found! Using /cm/shared/apps/amber14/bin/mmpbsa_py_energy cpptraj found! Using /cm/shared/apps/amber14/bin/cpptraj Preparing trajectories for simulation... /cm/shared/apps/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0 warn('Solvated topology %s has IFBOX == 0' % ifbox) 5 frames were processed by cpptraj for use in calculation. Running calculations on normal system... Beginning GB calculations with /cm/shared/apps/amber14/bin/mmpbsa_py_energy calculating complex contribution... Atom 121 outside the allowed range of 1-2 Angstroms for igb==7. ... regenerate prmtop with 'bondi' radii! File "/cm/shared/apps/amber14/bin/MMPBSA.py.MPI", line 96, in app.run_mmpbsa() File "/cm/shared/apps/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa self.calc_list.run(rank, self.stdout) File "/cm/shared/apps/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run calc.run(rank, stdout=stdout, stderr=stderr) File "/cm/shared/apps/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run self.prmtop)) CalcError: /cm/shared/apps/amber14/bin/mmpbsa_py_energy failed with prmtop 6058_rep0_pose11_dimer_stripWIG.prmtop! 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. --------------------------------------------------------------------------