Dear Amber experts,
Computer reports error in my input file for MD run.
I need your help how to correct my input file.
See details below.
Thank you,
Michael
Input file: heat1.in
protein restraint, heating 50K
&cntrl
imin=0,
ntx=1,
irest=0,
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=50000,
ntt=3,
gamma_ln=1.0,
ntr=1,
ig=-1,
ntpr=100,
ntwr=10000,
ntwx=100,
dt=0.002,
nmropt=1,
ntb=1,
ntp=0,
cut=10.0,
ioutfm=1,
ntxo=2,
/
&wt
type='TEMP0',
istep1=0,
istep2=50000,
value1=0.0,
value2=50.0
&wt type='END' /
Hold protein fixed
10.0
RES 1 509
/
&rst
restraint = "distance( (5716) (6163) )"
restraint = "distance( (1297) (6163) )"
restraint = "distance( (5756) (6163) )"
restraint = "distance( (5348) (6163) )"
restraint = "distance( (5134) (6163) )"
restraint_wt = 50.0
/
Submitted job:
nohup mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i heat1.in -o heat1.out -p ../*.prmtop -c ../2_/*.rst -x heat1.mdcrd -r heat1.rst -ref ../2_/*.rst &
[1] 16844
[enzyme03] 578 : namelist not terminated with / or &end
Bad data for namelist object value2
Cannot match namelist object name restraint
namelist read: misplaced = sign
Cannot match namelist object name "distance
Cannot match namelist object name (
Cannot match namelist object name (5716)
Cannot match namelist object name (6163)
Cannot match namelist object name )"
Cannot match namelist object name restraint
namelist read: misplaced = sign
Cannot match namelist object name "distance
Cannot match namelist object name (
Cannot match namelist object name (1297)
Cannot match namelist object name (6163)
Cannot match namelist object name )"
Cannot match namelist object name restraint
namelist read: misplaced = sign
Cannot match namelist object name "distance
Cannot match namelist object name (
Cannot match namelist object name (5756)
Cannot match namelist object name (6163)
Cannot match namelist object name )"
Cannot match namelist object name restraint
namelist read: misplaced = sign
Cannot match namelist object name "distance
Cannot match namelist object name (
Cannot match namelist object name (5348)
Cannot match namelist object name (6163)
Cannot match namelist object name )"
Cannot match namelist object name restraint
namelist read: misplaced = sign
Cannot match namelist object name "distance
Cannot match namelist object name (
Cannot match namelist object name (5134)
Cannot match namelist object name (6163)
Cannot match namelist object name )"
Cannot match namelist object name restraint_wt
namelist read: misplaced = sign
Cannot match namelist object name 50.0
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 16845 on
node enzyme03 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
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Received on Mon Feb 20 2017 - 05:00:03 PST
