Re: [AMBER] Practical questions on NMR-refinment

From: David A Case <>
Date: Wed, 3 Mar 2021 21:31:08 -0500

On Wed, Mar 03, 2021, Gustavo Seabra wrote:
>I have been asked to use MD to help assign some structures according to NMR
>and NOESY data. All I have is a table showing the assignment of NOESY peaks
>(the protons names) and the intensities (volumes) for each peak. Something
>Unit1# resname H Unit2 resname H Intensity
>1 DhAla H3b 2 NOHAla H2 1.00
>1 DhAla H3b 5 4MePro H2 0.11
>1 DhAla H3b 5 4MePro H5b 0.04
>1 DhAla H3b 3 NMeAsn NMe 0.04
>I am in the process of converting this data into the 7-column format
>required by makeDIST_RST to create the actual NMR-restraints. I'd
>appreciate some input on the practical aspects of this:

Note that the 7-column format requires a upper bound to the distance, *not*
a NOESY intensity. So you will need to work with the people that
provided the data to make this conversion. Most NMR software pipelines
can do this: find some peaks with known distances, and use their intensities
as a calibration.

>1. Some signals appear twice (from the peak above and below the diagonal),
>only with the atoms inverted, but not necessarily with the same intensity.
>For example, I may have:
>1 DhAla H3b 3 NMeAsn NMe 0.04
>3 NMeAsn NMe 1 DhAla H3b 0.12

Again, this is a question for the people who collected and processed the

>4. Finally, is there an advantage for using the intensities instead of
>lower/upper distance bounds? Or vice-versa?

Using intensities is possible in sander, but is definitely an advanced
topic. Basically, this sort of analysis went out of fashion once it became
routine to get isotopically-labelled samples. It would only be of interest
now if you had build-up curves (NOESY spectra as a function of mixing time.)
Such experiments are key to the so-called exact-NOE method. Even then, one
would certainly do a distance-based structure analysis first.

...hope this helps...dac

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Received on Wed Mar 03 2021 - 19:00:02 PST
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