Dear AMBER developers,
I have a few questions concerning NOE distance constraints during MD
simulations of small cyclic peptides. I'm not running the MD jobs
myself but I'm in charge of preparing the distance files according to
the NOE contacts observed in the 2D-NMR spectra.
My first question concerns diastereotopic assignments of prochiral
protons (e.g. alpha protons in a glycine residue): how can I label
them? According to "map.dgIUPAC"
(
http://archive.ambermd.org/201009/att-0820/map-DG_modified.ABMBER), I
could name the pseudoatom either "QPA" or "QA": which one label should
I use? Is there any difference? Should I use an averaged distance
constraint?
My second question is the following. Let's assume I have two prochiral
protons (again not diastereotopically assigned, let's name them H1 and
H2), and I know from NMR data that:
a) either H1 or H2 shows a NOE contact with proton X;
b) the other one shows a NOE contact with proton Y.
In this case I have specific assignments but I don't know which one
proton is giving which one contact. The contacts are either H1-X/H2-Y
or H2-X/H1-Y. Is there a way to label this particular case in the
seven-column distance file? (of course I could just label both
contacts as pseudoatoms, but I would lose an important piece of
information, right?)
You can find some details about the simulation protocols in the attached file.
That's it, I hope I've been clear enough!
Thanks a lot for your attention.
Best regards,
Marco Bartoloni
(University of Bern)
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Received on Thu Aug 18 2011 - 04:00:02 PDT
