AMBER Archive (2009)

Subject: Re: [AMBER] nmr refinement of dimer

From: Therese Malliavin (terez_at_pasteur.fr)
Date: Wed Feb 11 2009 - 04:57:06 CST

Hello Sally,

If you are interested to perform NMR refinement on symmetric dimers, you
may be interested to try the software ARIA:
aria.pasteur.fr, which is dedicated to this problem.

Hope it helps,

Therese Malliavin
Unite de Bioinformatique Structurale
Institut Pasteur, Paris
France

Sally Pias wrote:
> Hello,
>
> 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.
>
> Any insights or suggestions?
>
> Thank you,
>
> Sally Pias
>
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