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

From: Thomas Pochapsky <>
Date: Tue, 12 Jul 2016 08:36:35 -0400

It was indeed! Thanks!

On 7/11/16 9:36 PM, David A Case wrote:
> 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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