Re: [AMBER] Calculation of NMR relaxation rates

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 4 Dec 2013 09:17:00 -0700

Hi,

There is an unfortunate typo in the manual; the frequency should be given
in MHz, not Hz. Try using 500 instead of 500000000 for the 'freq' keyword.

-Dan

On Mon, Dec 2, 2013 at 5:43 PM, Mahendra B Thapa <thapamb.mail.uc.edu>wrote:

> Dear Amber users
>
> I used the following input to calculate NMR relaxation rates (R1 and R2)
> of backbone N-H bonds of a protein using amber 12 with cpptraj :
>
> trajin test_file1.pdb
> vector v0 .15 ired @16
> vector v1 .107 ired @108
> ...............................................
> matrix ired name matired order 2
> diagmatrix matired vecs 72 out ired.vec name modes_name
> ired relax freq 500000000 NHdist 1.02 order 2 tstep 1.0 tcorr 4000.0
> out v0.out norm modes modes_name noefile noe_NH_test_Protein
> go
>
> I am interested to find these relaxation rates at 500MHz. Though R1 values
> are comparable to the experimental results but *R2 value is quite high for
> all vectors* , such as
>
> vector R1 R2 NOE
> 0 47.73492 22659.00760 1.00000
> 1 39.87131 29025.85386 1.00000
>
> I did 50ns all-atom simulation, so I choose tcorr as 4000.0 . Any
> suggestion and comment will help me.
>
> Thank you
> Mahendra Thapa
> University of Cincinnati,OH
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>



-- 
-------------------------
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 04 2013 - 08:30:03 PST
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