AMBER Archive (2005)

Subject: Re: AMBER: Dipolar coupling refinement

From: David A. Case (case_at_scripps.edu)
Date: Fri Oct 21 2005 - 20:03:43 CDT

On Fri, Oct 21, 2005, s0344557_at_sms.ed.ac.uk wrote:
>
> I am trying to use the residue dipolar coupling(RDC) constants to refine my
> tetrasaccharide. I prepared the RST-AC.f manully with 10 RDCs of two rings and
> the alignment saupe parameters are from one of the best fitting results of the
> RDCs to the structure. But when running the refinement with this restraint, I
> did not improve the structure at all.

Your table of computed vs. experimental RDC's looks pretty good: you have a
linear correlation of 0.98 between calculated and observed values, and there
is only 1.6 kcal of energy in this penalty function. That only gives a very
weak bias towards forcing agreement with experiment:

> Residual dipolar splittings:
>
>
> ------------------------------------------------------------------------------
> First atom Last atom curr. value target deviation penalty distance
> ------------------------------------------------------------------------------
> C2 TAP 1 -- H6 TAP 1: -1.952 -3.400 1.448 0.210 1.090
> C1 TAP 1 -- H7 TAP 1: 6.432 5.800 0.632 0.040 1.090
> C5 TAP 1 -- H9 TAP 1: 7.247 6.100 1.147 0.131 1.090
> C6 TAP 1 -- H10 TAP 1: 7.492 5.400 2.092 0.438 1.090
> C3 TAP 1 -- H4 TAP 1: 6.946 6.200 0.746 0.056 1.090
> C13 TAP 1 -- H17 TAP 1: 4.388 5.100 -0.712 0.051 1.090
> C14 TAP 1 -- H18 TAP 1: -1.570 -3.100 1.530 0.234 1.090
> C15 TAP 1 -- H19 TAP 1: -3.248 -3.000 -0.248 0.006 1.090
> C18 TAP 1 -- H25 TAP 1: -2.836 -4.800 1.964 0.386 1.090
> C16 TAP 1 -- H24 TAP 1: -2.634 -3.600 0.966 0.093 1.090
> Total align constraint: 1.64
> # Pearson r rms error
> -----------------------------------
> Align correlation: 10 0.98325 2.38706 1.28233

If you really want to force a tighter fit (and some of the deviations are
fairly large) you will need to increase the weight of this penalty function by
increasing the dwt values.

...good luck...dac
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