Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
set sim = 2BDM_tmionly/angle
set mpirun = mpirun -np 32 -machinefile /uufs/updraft.arches/host/var/torque/aux//202692.uprm.privatearch.arches
set pmemd = ~/pmemd-a10-updraft 
set cur = 40
set pre = 39
cd ~/biodata2/P450/2BDM_tmionly/angle
mpirun -np 32 -machinefile /uufs/updraft.arches/host/var/torque/aux//202692.uprm.privatearch.arches /uufs/chpc.utah.edu/common/home/u0181375/pmemd-a10-updraft -O -i mdin -o mdout.40 -p prmtop -c restrt.39 -r restrt.40 -x traj.40 -e ener.40
Warning: Permanently added 'up055,172.17.22.55' (RSA) to the list of known hosts.
Warning: Permanently added 'up054,172.17.22.54' (RSA) to the list of known hosts.
=>> PBS: job killed: walltime 39601 exceeded limit 39600
Terminated
Killed by signal 15.
Killed by signal 15.
Killed by signal 15.