AMBER Archive (2008)

Subject: AMBER: Correlation functions from iRED analysis

From: Samuel Genheden (a03samge) (a03samge_at_student.his.se)
Date: Thu Jun 19 2008 - 05:22:53 CDT

Hello, Amber users

I'm studying a protein using MD and would like to calculate correlation functions with the iRED method in order to compare order parameters from NMR. My protein is 138 residues long and contains 10 prolines, and therefore I have 128 N-H vectors. I'm using Amber10. My input file looks like this:

trajin ../mdcrd5.gz
trajin ../mdcrd6.gz
vector v2 :2_at_N ired :2_at_H
vector v3 :3_at_N ired :3_at_H
..
vector v138 :138_at_N ired :138_at_H
matrix ired name matired order 2
analyze matrix matired vecs 128 out ired.vec
vector v2 :2_at_N corrired :2_at_H order 2 modes ired.vec beg 1 end 128 npair 1
vector v3 :3_at_N corrired :3_at_H order 2 modes ired.vec beg 1 end 128 npair 2
..
vector v138 :138_at_N corrired :138_at_H order 2 modes ired.vec beg 1 end 128 npair 128
analyze timecorr vec1 v2 tstep 10.0 tcorr 10000 out Ired/v2.out
analyze timecorr vec1 v3 tstep 10.0 tcorr 10000 out Ired/v3.out
..
analyze timecorr vec1 v138 tstep 10.0 tcorr 10000 out Ired/v138.out

(I've have also tried to break it up in two ptraj scripts, since the manual is a little bit vague if this is neccessary.) The problem is that all the correlation functions calculated, v2.out, v3.out, .. v138.out is the same, i.e. all the output files contains the same numbers. What am I doing wrong? I can hardly believe that all the correlation functions should be identical.

And when I'm at writing - what is the best way to obtain the order parameters from the correlation functions?

Best regards, Samuel

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