Try not indenting the &rst block?
Bill
On 2/20/17 4:47 AM, Michael Shokhen wrote:
> 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).
>
> --------------------------------------------------------------------------
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 20 2017 - 05:00:03 PST
