Re: [AMBER] Practical questions on NMR-refinment

From: Gustavo Seabra <>
Date: Thu, 4 Mar 2021 11:56:18 -0500

On Wed, Mar 3, 2021 at 9:31 PM David A Case <> wrote:

> On Wed, Mar 03, 2021, Gustavo Seabra wrote:
> >
> >I have been asked to use MD to help assign some structures according to
> >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
> >like:
> >
> >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.

I was under the impression I could use the intensities with the `-vol`
option, as described in page 554:

"The format for the -vol option is the same as for the -upb option except
that the seventh column holds a peak
intensity (volume) value, rather than a distance upper bound."

Did this feature change? Or am I understanding it wrong?

Still, if I understand correctly, the best option is to use the distances,
I'll talk to them to see if I could get some better data, then.


> >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
> data.
> >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 Thu Mar 04 2021 - 09:00:02 PST
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