i've had this problem with NAMELIST before. i think it might be a
problem with your input file. try changing the &end in your file to /
and it should fix this problem
On 7/13/07, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > In submitting a job to run on AMBER, this is the script I
> > used:
> ...
>
> Your PBS script looks OK except for a couple of things...
>
> > mpirun -np 4 $AMBERHOME/exe/sander -O -i bundlewat.in -p ...
>
> You are referencing "sander" which normally refers to the sequential
> version (so it would effectively just run on one node). Perhaps you mean
> to run sander.MPI (or perhaps sander.MPI was renamed to sander).
>
> > (19): invalid reference to variable in NAMELIST input, unit 5, file
>
> This states that you have a problem with your "mdin" file, something in
> there that is not recognized as a AMBER input option. If you post the
> mdin file, we may be able to figure out, otherwise, carefully check to see
> that none of the keywords are misspelled or anything...
>
> -- tec3
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Received on Wed Jul 18 2007 - 06:07:50 PDT
