AMBER Archive (2008)

Subject: SV: AMBER: Correlation functions from iRED analysis

From: Samuel Genheden (a03samge) (a03samge_at_student.his.se)
Date: Thu Jun 19 2008 - 10:53:29 CDT

Hello,
 
I have 138 residues in my protein but I have 20 prolines on which there is no N-H vector so I'm only defining 128 vectors, although the names of the vectors follows the residue number so the last vector is named v138. I think that the names of the vectors should not matter, or?
 
/ Samuel

________________________________

Från: owner-amber_at_scripps.edu genom fatima.chami_at_durham.ac.uk
Skickat: to 2008-06-19 15:43
Till: amber_at_scripps.edu
Ämne: RE: AMBER: Correlation functions from iRED analysis

Hi Samuel,

Quoting "Samuel Genheden (a03samge)" <a03samge_at_student.his.se>:

> Helo,
>
> I still get identical correlation functions for all the N-H vectors, even
> though I do a RMS fit. And I thought one of the advantages of doing an iRED
> analysis was that I should not do an RMS fit. Isn't that correct

likewise, I thought there is no need to alignment of the snapshots
it is so vague in the manual... I am having the same issue with this cal.

 is it 128 N-H vectors or 138 cause your script shows 138 N-H vectors and
compute 128 eigenvectors ...should not they be same number!

best wishes
fatima
>
> / Samuel
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu on behalf of Myunggi Yi
> Sent: Thu 6/19/2008 2:52 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Correlation functions from iRED analysis
>
> On Thu, Jun 19, 2008 at 6:22 AM, Samuel Genheden (a03samge) <
> a03samge_at_student.his.se> wrote:
>
> >
> > 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?
> >
>
> To get the generalized order parameters, you need to calculate
> auto-correlation functions after "rms fitting".
> Then fit your graph with single or double exponential functions.
> The plateau corresponds to the S^2.
>
> >
> > Best regards, Samuel
> >
>
>
>
> --
> Best wishes,
>
> Myunggi Yi PhD
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
>
> 

--
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
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