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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 11 Dec 2013 16:10:24 -0700

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)
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Received on Wed Dec 11 2013 - 15:30:02 PST
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