AMBER Archive (2008)

Subject: Re: AMBER: RDCs in AMBER 10

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 12 2008 - 17:56:52 CST

On Tue, Feb 12, 2008, Douglas Kojetin wrote:
>
> Will AMBER 10 provide support for residual dipolar couplings other
> than backbone N-H and Ca-H and, although less important, step-by-step
> weight changes of dwt for RDCs [ http://structbio.vanderbilt.edu/
> archives/amber-archive/2007/3787.php ] ?

Amber 9 (or 10) are not limited to NH and CaH RDC's: you can use whatever
nuclei pair you want (including H-H RDC's, for example). Take a look at the
files in amber9/test/rdc: this shows RDC's applied to a nucleic acid. The
same ideas could be used for any RDC, as far as I can see.

Amber 10 will also allow for CSA (or pseudo-CSA) constraints to be defined;
these are quite similar to RDC's in their information content.

Using weight changes to ramp dwt up or down has not yet been added. But
thanks for reminding me again about this.

....regards...dac

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