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 NH 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: owneramber_at_scripps.edu genom fatima.chami_at_durham.ac.uk
Skickat: to 20080619 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 NH 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 NH vectors or 138 cause your script shows 138 NH vectors and
compute 128 eigenvectors ...should not they be same number!
best wishes
fatima
>
> / Samuel
>
>
> Original Message
> From: owneramber_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 NH 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
> autocorrelation 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) 6451334
> 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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