AMBER Archive (2008)

Subject: Re: AMBER: Using RDCs for structure refinement

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Aug 12 2008 - 11:36:24 CDT

On Tue, Aug 12, 2008, David Witte wrote:

> >I completed a structure calculation with CYANA using distance
> >restraints derived from NOESY spectra and dihedral angles as input.
> >I started the structure refinement with Amber8 using the final CYANA
> >output for these calculation. Now I want to use RDCs in addition to
> >the distance restraints and the dihedral angles as input, But the
> >calculation gives the exact same result with and without RDCs (RMSD
> >and violated constraints) indicating that Amber8 does not use the
> >RDCs as input. Also Amber8 reports in the logfile the same number of
> >constraints used for structure refinement with and without RDCs as
> >input. The RDC part of my restraints file looks like this:

What value of nmropt are you using? You should probably post the entire
input file, not just the RDC part.

...dac

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