On Mon, Jun 13, 2016, tanfei777.sina.cn wrote:
> the predefined upper distance bounds are 2.8 (as in the example
> below),and the group averaged result is r3= 5.71, is this enlargement
> of upper distance restraint mainly due to 1/r(-6) group averaging as
> indicated in igr1 and igr2?
Yes.
> Where do I change the IR6 value?
In an &rst namelist block. This is a "sticky" assignment: if you give a value
in one &rst block, that value will continue to be used for subsequent &rst
blocks, unless/until you assign it a different value.
> And is there is a possibility of turning off group averaging and use
> upper distance bounds as predefined by user.
You can manually edit the upper bound to whatever value you want. But
averaging will still take place whenever you set iat values to -1.
Note that the "ambiguous" capability in Amber is of a limited sort: it
assumes that you have chemical shift near-degeneracy, so that you can't
uniquely assign a peak to a single proton. Peaks that might belong to
a large number of protons (in either dimension) then effectively become
nearly useless as restraints.
Amber does not have the capability to describe more general ambiguities:
such as if (from other evidence) you wish to assign a certain cross peak
to either atoms (5 to 12) OR to atoms (17 to 32). If only one of these
two distances is short, you can put them in as independent restraints,
setting ialtd=1 for those restraints. Then the distance that is short
will be "active" and the distance that is long will be ignored. This
scheme works less well if both distances are short, since both will be
"active", which is presumably not what you want.
...hope this helps....dac
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Received on Mon Jun 13 2016 - 11:00:04 PDT
