Hello,
I have a question, though this is not new, let me put the difficulty that I am
facing.
I am using Multiple RDCs, N-H (1DNH) and N-C' (2DNC'), to refine a structure. I
refined it with N-H RDCs, the problem here is refining with N-C RDCs.
As explained in the RDCPot tools and input file from of gb1_rdc
(sa_tmv_bice_rgyr.inp), I scaled the N-C' RDCs with 8.33 factor and then
refined using the following script:
!-----------------------------------------------------------------------------------
evaluate ($ksani = 0.01) ! overall dipolar force constant
evaluate ($ksani_NC = 0.050*$ksani)
!set echo off message off end
!----read dipolar coupling restraints and CSA----------
sani {* HN RDCs *}
nres=1000
class p_nh
force $ksani
potential harmonic
coeff 0.0 -5.00 0.33
@tbl/rdc_n.tbl
class p_nc
force $ksani_NC
potential harmonic
coeff 0.0 -5.0 0.33
@tbl/rdc_nc.tbl
end
!--------------------------------------------------------------
But all my N-C' RDCs are violated using the above approach. I Qsaupe is quiet
high, even after refinement with N-C' RDCs. Can anyone help me in this regard.
Can anyone also explain me why we use 0.05*ksani for N-C' instead of
0.120*$ksani.
The following are the input lines I used for pales:
for N-H:
45 Leu N 45 Leu HN -0.773 1.000 1.00
46 Met N 46 Met HN 3.230 1.000 1.00
47 Val N 47 Val HN -1.933 1.000 1.00
for N-C':
45 Leu C 46 Met N 2.260 0.120 8.33
46 Met C 47 Val N -0.152 0.120 8.33
47 Val C 48 Leu N -1.753 0.120 8.33
Additionally, I have even tried without scaling N-C' RDCs but still get similar
violations.
Thank You,
Chaitanya.
Sai Chaitanya Chiliveri
Ph.D Student,
NMR Facility,
Centre for Cellular and Molcular Biology,
Hyderabad, Andhra Pradesh, INDIA - 500007
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