[AMBER] Calculation of NMR relaxation rates

From: Mahendra B Thapa <thapamb.mail.uc.edu>
Date: Mon, 2 Dec 2013 19:43:10 -0500

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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Received on Mon Dec 02 2013 - 17:00:03 PST
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