Re: [AMBER] Does anyone knows how to generate an ired vector

From: 肖立 <xiaoli19871216.gmail.com>
Date: Wed, 11 Dec 2013 15:49:47 -0800

Hi, Dan:
    Thank you for your answer. However, in our problem, we need to analyze
the autocorrelation function of N-H bond over almost 500 residues. Hence,
it seems that it is not a clever way if we type 500 lines to generate these
vectors. Do you have a cleverer way to do it?
Thanks a lot!
Li


On Wed, Dec 11, 2013 at 3:10 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> The IRED procedure involves defining the IRED vectors, creating an IRED
> matrix, diagonalizing the IRED matrix, then finally performing the IRED
> analysis. The following is an example for performing IRED analysis in
> CPPTRAJ for 4 N-H vectors:
>
> trajin 1IEE_A_test.mdcrd
> vector v0 .25 ired @26
> vector v1 .41 ired @42
> vector v2 .61 ired @62
> vector v3 @68 ired @69
> matrix ired name matired order 2
> ###Attention: adjust vecs to number of residues in your protein
> diagmatrix matired out ired.vec name ired.vec vecs 4
> ired relax freq 500.0 NHdist 1.02 tstep 1.0 tcorr 10000.0 norm out v0
> noefile noe \
> order 2 modes ired.vec orderparamfile orderparam
>
> You will of course have to adjust parameters (such as vecs, tcorr, tstep,
> freq etc) to fit your particular system.
>
> Hope this helps.
>
> -Dan
>
>
>
> On Wed, Dec 11, 2013 at 3:51 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
>
> > Hi, all:
> > I use the comment
> > trajin ***.mdcrd
> > vector ired_vector :1-468 ired 1:468 out ired_vector.dat
> >
> > to generate an ired vector.
> > The program shows it can read the program and run it smoothly. However,
> > there is no output file.
> > I'm wondering if anyone knows what is wrong and how to generate an ired
> > vector correctly.
> >
> > Best,
> > Li
> > --
> > Li Xiao
> > University of California, Irvine
> > Email: xiaoli19871216.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Wed Dec 11 2013 - 16:00:03 PST
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