On Mon, Mar 16, 2015 at 1:49 PM, Vijay Achari <glycoamber.gmail.com> wrote:
> HI Dan,
>
> The command I used was:
>
>
>
> for i in {1..128};do
>
> cpptraj $top <<EOF
> trajin $path/reImaged-bcmLyo25perR.nc 15001 60000 #60000
>
> vector v1 principal z
> vector v2 :$i.C52 :$i.C61
> vector v3 :$i.C64 :$i.C69
>
> vectormath vec1 v1 vec2 v2 out dataFiles-only/angleZ-chainC12-lipid-$i.dat
> name AngleZ-C12 dotangle
> vectormath vec1 v1 vec2 v3 out dataFiles-only/angleZ-chainC8-lipid-$i.dat
> name AngleZ-C8 dotangle
>
> EOF
>
> done
>
>
>
> Previously there was white space after z. That's why it showed [z ] in the
> error before. Once the white space fixed, the calculation run fine.
>
​What kind of whitespace was it? Was it a carriage return? A tab?
cpptraj splits argument lists on whitespace. So it's possible that *some*
whitespace characters (like weird half-DOS-line-endings, tabs, or something
else?) that *renders* as whitespace could cause this problem.
It would be nice to know what that character was, though, so this problem
can be fixed.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 16 2015 - 11:00:08 PDT
