AMBER Archive (2009)

Subject: Re: [AMBER] nmr refinement of dimer

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Feb 12 2009 - 07:08:08 CST

On Thu, Feb 12, 2009, Sally Pias wrote:

> I have already defined every distance restraint as ambiguous, with
> equivalent atoms in both protomers able to satisfy the restraint.
> However, I do not understand clearly how group coordinate averaging is
> used. Does the coordinate averaged "atom" position actually fall
> halfway between the two atoms defined in the ambiguity?

No. Assuming that ir6 is set (the default) the distance is the r**-6
average of the two (or more) distances involved in the ambiguity. This
is really the same as what Aria does, for example. In this procedure, a
short distance will be "active" and a longer distance will effective be
ignored.

> I am working with a homology-modeled starting structure. After a few
> rounds of a simple simulated annealing protocol (based on the manual
> example and Tutorial A4), first in vacuum and then with GB solvent, I
> have very few larger violations (between 0.5 and 1.5 A, possibly
> indicating errors in the NOE list) but many smaller violations
> (between 0.2 and 0.5 A). I am not sure yet whether this is an effect
> of working with a homology modeled starting structure or whether the
> ambiguities may be introducing a structural distortion. The
> structures look reasonable after simulated annealing, but I am still
> suspicious.

It's hard to say much from afar. Having lots of violations between 0.2
and 0.5 Ang. is indeed suspicious, but you want to fix the assignment
errors (if they are indeed present) first. It might be worth setting
ialtd=1 and re-running the refinement, to see what sort of difference
that makes.

....dac

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