Re: [AMBER] S2 order parameter not being calculated in IRED analysis.

From: Gupta, Arun <>
Date: Tue, 15 Dec 2020 09:11:47 +0000


It appears to me that there are some proline residues in the whole set of NH vectors used as input. Try to remove those residues in the script. I think, then it should work fine.



Arun Gupta PhD, MRSC
Research Fellow
Challis & Lewandowski Group
Chemistry Department
University of Warwick
Gibbet Hill Road
Coventry CV4 7AL
United Kingdom
From: Chetna Tyagi <>
Sent: Friday, December 11, 2020 1:14 PM
To: AMBER Mailing List <>
Subject: [AMBER] S2 order parameter not being calculated in IRED analysis.

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 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
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Received on Tue Dec 15 2020 - 01:30:03 PST
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