Hello All,
I try to calculate generalized order parameters (S2) and NOE of each
residue (N-H vector) from a molecular dynamics trajectory.
The system is a little protein of 155 amminoacid and the simulation is
500ns long.
I'm using the iRED method as described in the manual but i get very
strange value
for the NOE instead for S2 i get a very good correlation versus the
experimental order parameters.
The script for NOE calculation was like this :
====================================
trajin Traj.mdcrd 1 125000 1
vector v2 :2.N corrired :2.H order 2 modes ired.vecs beg 1 end 145 npair 1
vector v3 :3.N corrired :3.H order 2 modes ired.vecs beg 1 end 145 npair 2
vector v4 :4.N corrired :4.H order 2 modes ired.vecs beg 1 end 145 npair 3
...
....
....
vector v155 :155.N corrired :155.H order 2 modes ired.vecs beg 1 end 145
npair 145
analyze timecorr vec1 v2 relax NHdist 1.02 freq 500 out OutPut.nh norm
noefile Noe_Calc.noe
====================================
the ired.vecs were calculated before for S2. The NOE value are all
negative :
****************************************
- Calculated relaxation rates and NOEs -
****************************************
vector R1 R2 NOE
0 1.07972 1.13005 -2.46742
1 1.43791 1.54210 -1.82056
2 1.35727 1.44151 -2.00349
3 1.16927 1.22846 -2.33308
4 1.37891 1.48687 -1.74414
5 1.36801 1.46610 -1.86150
6 1.07659 1.14031 -2.15212
7 1.37379 1.48138 -1.73555
8 1.34011 1.42880 -1.95643
9 1.36118 1.45175 -1.89964
10 1.39956 1.49967 -1.81208
11 1.43605 1.54495 -1.74365
12 1.33190 1.40948 -2.10905
13 1.26713 1.34012 -2.13496
14 1.33406 1.43197 -1.85110
15 1.30450 1.39944 -1.89704
16 1.33292 1.41641 -2.04943
17 1.24387 1.32357 -2.06067
18 1.34503 1.44692 -1.77198
19 1.36764 1.46742 -1.80180
20 1.36245 1.46682 -1.71877
21 1.32079 1.41449 -1.83517
22 1.34298 1.45133 -1.64901
23 1.58521 1.75122 -1.17599
24 1.48358 1.61158 -1.51470
25 1.43603 1.54483 -1.68576
26 1.38172 1.47545 -1.84681
27 1.47620 1.61116 -1.39997
28 1.55606 1.71249 -1.22541
29 1.34758 1.44745 -1.73006
30 1.44572 1.58926 -1.30080
31 1.42548 1.55284 -1.45083
32 1.28602 1.36892 -1.95652
33 1.51896 1.66069 -1.35449
....
....
....
Someone have experience in NOE calculation and could give me some hints ?
thanks a lot
max
--
Dr. Massimiliano Meli, Ph.D
Istituto di Chimica del Riconoscimento Molecolare, CNR
web:http://colombo-biocomputing.org/
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Received on Tue Nov 13 2012 - 02:30:04 PST
