Re: [AMBER] predicting RDCs for un-restrained bonds

From: David A Case <>
Date: Mon, 11 Jul 2016 21:36:38 -0400

On Mon, Jul 11, 2016, Thomas Pochapsky wrote:
> Is there a way of getting a listing of predicted RDC values for all NH
> bonds in a protein given a best-fit alignment tensor, even if there
> aren't restraints on all NH bonds?

If I understand your question: Do a minimization with RDC restraints for
the NH bonds that provide the experimental data. Set freezemol=.true., so the
only thing you are optimizing is the alignment tensor. The minimization
should converge very quickly. Assuming you have set


in your input, you will get a list of predicted (and observed) NH RDC's
at the end, along with info about the optimized alignment tensor.

If you want info on NH bonds for which you don't have experimental data,
just set the observed value to zero (or to any value, really), and set
the "dwt" value (the restraint weight) for those NH bonds to zero. That
way, those NH bonds won't affect the alignment tensor calculation, but the
output will include the calculated values.

...hope this is what you were after....dac

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Received on Mon Jul 11 2016 - 19:00:02 PDT
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