Hi,
Try adding the keyword 'orderparamfile <name>' to your 'ired' command, e.g.
ired relax NHdist 1.00 freq 500.0 tstep 0.002 tcorr 10.0 modes
ired.vec out v0.out noefile noe order 2 orderparamfile s2.dat
Not sure why that was omitted from the manual. I'll have to fix that.
The manual does mention that the order parameter data set is created
with name:
<name>[S2]
So you could always ask cpptraj to create that data file with the
'create' command after the 'ired' command, e.g.:
create s2.dat <name>[S2]
Hope this helps,
-Dan
On Fri, Dec 11, 2020 at 8:49 AM Chetna Tyagi <cheta231.gmail.com> wrote:
>
> Dear AMBER users,
>
> Upon running the below pasted IRED script. The output file does not contain
> the S2 order parameter column. It only has the plateau and TauM values.
>
> Moreover, my NH vector NOE lie in the range of -3 to -2 while an old paper
> describes them as positive values. I have tried different window sizes for
> the calculation but still majorly the same result.
>
> Please advice as to what could be missing.
>
>
>
>
>
>
>
>
> *parm ww1amt.prmtoptrajin AMD-t.nc# Define N-H IRED vectorsvector v0 .7
> ired .8vector v1 .34 ired .35vector v2 .47 ired .48........*
>
>
>
>
>
>
>
>
>
>
> *vector v16 .249 ired .250vector v17 .266 ired .267# Define IRED matrix
> using all previous IRED vectorsmatrix ired name matired order 2#
> Diagonalize IRED matrixdiagmatrix matired vecs 18 out ired.vec name
> ired.vec# Perform IRED analysisired relax NHdist 1.00 freq 500.0 tstep
> 0.002 tcorr 10.0 modes ired.vec out v0.out noefile noe order 2*
>
> --
> Best wishes
> Chetna
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Received on Tue Dec 15 2020 - 07:30:03 PST
