On Fri, Mar 05, 2010, Danny Xu wrote:
>
> Can anyone provide some info on how to calculate residual dipolar
> couplings (RDC) from amber MD trajectories?
It's not clear how much you have read: Section 6.5 in the Amber10 Users'
Manual covers this subject. There are example calculations in
$AMBERHOME/test/rdc.
If you set your restraint weights to zero and dcut to a negative number,
the code will print out the rdc values. If you wanted to do this for
every snapshot in a trajectory, you could probably use the imin=5 option.
An alternative is to use ptraj to create PDB files of selected snapshots
of your protein, then feed those to one of the many programs that compute
RDC's from structure (e.g. from the Tolman, Prestegard or Al-Hashimi groups.)
...good luck....dac
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Received on Sat Mar 06 2010 - 07:00:02 PST
