AMBER Archive (2009)

Subject: Re: [AMBER] nmr refinement of dimer

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Feb 11 2009 - 07:02:37 CST

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.

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

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