On Thu, Aug 18, 2011, marco.bartoloni.students.unibe.ch wrote:
>
>
> 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?
I recommend you use map.DG-AMBER, since the others have not been tested much.
If you know the pro-chiral assignments, use "HA2" and "HA3". If you don't
have a stereospecific assignment, either "QPA" or "QA" can be used; they
mean the same thing. What sort of restraint you use depends on the value of
ir6, and you probably want to do some testing to be sure you are getting what
you want.
>
> 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?)
My recollection is that Amber doesn't directly support this sort of partial
assignment. You could try using the "altdis" sort of restraint, but one would
again have to run tests and be very careful. You might find that structures
that arise using pseudoatoms would actually fall into one of the two
categories above, effectively suggesting the correct assignment.
...dac
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Received on Thu Aug 18 2011 - 05:00:02 PDT
