AMBER Archive (2008)

Subject: AMBER: Using RDCs for structure refinement

From: David Witte (david.witte_at_uni-konstanz.de)
Date: Tue Aug 12 2008 - 02:52:53 CDT

> Hi,
> 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:
>
> &align
> ndip=25,dwt=1.0,
> gigj=-3.1631,
> dij=1.041,
> dcut=-1.0,freezemol=.false.,
> id(1)=241, jd(1)=242, dobs(1)= 3.69,
> ....
> &end
> Does anyone know what I'm doing wrong?
> Thanks,
> David Witte

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