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
