AMBER Archive (2008)

Subject: Re: AMBER: cross correlation function using iRED matrix

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Wed Jun 18 2008 - 13:07:03 CDT

Hi,

On Wed, Jun 18, 2008 at 1:07 PM, <fatima.chami_at_durham.ac.uk> wrote:

>
> Hi folks,
>
> I am trying to calculate the cross correlation time function according to
> the
> ired approach. The ired eigen vector file shows undefined values:
>
>
> Eigenvector file: IRED
> 2 2
> 1.00000 1.00000
> ****
> 1 1.10699
> -0.70711 0.70711
> ****
> 2 0.89301
> -0.70711 -0.70711
>
>
> my ptraj script is as follow:
> -------------------------------------------------------
> trajin stack8w_md8_no_wat.mdcrd
> rms first

>> If you do "rms fit", you will remove the overall-rotational motion.
>> Don't superimpose your trajectories for iRED.

> vector v1 :4_at_C11 ired :4_at_O2
> vector v2 :5_at_C11 ired :5_at_O2
> matrix ired name residue_anal
> analyze matrix residue_anal vecs 6 out ired.vec thermo

>> vecs 2 (you have only two vectors)

>
> vector v1 :4_at_C11 corrired :4_at_O2 order 2 modes ired.vec beg 1 end 6 npair
> 1
> vector v2 :5_at_C11 corrired :5_at_O2 order 2 modes ired.vec beg 1 end 6 npair
> 2

>> beg 1 end 2

>
> analyze timecorr vec1 v1 vec2 v2 out vired.out
> ----------------------------------------------------------
>
> The logfile of ptraj
>
> Checking coordinates: stack8w_md8_no_wat.mdcrd
> ptraj(), analyzeMatrix: parameter "thermo" only
> works for MATRIX_MWCOVAR, returning.
> FYI: Number of read evecs is 2, number of requested evecs is 6
> WARNING in ptraj(), analyze timecorr: only calculating IRED corr for vec1,
> ignoring vec2
>
>
> best wishes
> Fatima
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-- 
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

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