[AMBER] Practical questions on NMR-refinment

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Wed, 3 Mar 2021 15:33:51 -0500

Hi all,

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:

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

In this case, what is the suggested approach? Should I keep only the
highest intensity one? the lowest? or take an average?

2. The intensities values are all relative to one particular peak,
arbitrarily set to intensity=1. Is that OK?

3. Some intensities are really low (e.g. 0.03). Are those important enough
to be included?

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

I'll greatly appreciate any help on this issue.

Thanks a lot!
Gustavo Seabra.
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Received on Wed Mar 03 2021 - 13:00:02 PST
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