AMBER Archive (2009)

Subject: Re: [AMBER] nmr refinement of dimer

From: Sally Pias (
Date: Thu Feb 12 2009 - 03:17:44 CST

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? I am
concerned because some of my ambiguities involve atoms from equivalent
residues on both protomers that are separated by 25 Angstroms. Is
coordinate averaging used mainly to determine whether a given distance
restraint is satisfied, or is it also used in the violation penalty
calculation? I have studied the Amber 9 manual pages (180-2 and
193-4) on this topic but do not yet have a clear picture of how it

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



On Wed, Feb 11, 2009 at 6:02 AM, David A. Case <> wrote:

> This is an example of an ambiguous restraint; input for these is
> discussed on p. 188 of the Users' Manual.
> [Note that Amber does not have the capability to enforce
> non-crystallographic symmetry between the two dimer structures,
> however.]
> ..hope this helps...dac
> On Wed, Feb 11, 2009, Sally Pias wrote:
>> I am wondering whether there is a way to carry out NMR refinement on a
>> dimeric system where ambiguities need to be defined across the two
>> monomeric units. For example, residue A has a distance restraint
>> involving residue Q, but it is unknown whether the restraint should be
>> applied between residues A and Q on the same protomer or between
>> residue A on one protomer and residue Q' on the other protomer.
>> Group coordinate averaging for such an ambiguity could lead to a
>> structural distortion, assuming that residues Q and Q' are fairly
>> distant from one another.

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