... how to convert the NOE volume to distance restraints?
There are many approaches people use to convert NOE volumes to distance restraints, ranging from very simple "binning" (weak/medium/strong) to more complex algorithms such as Mardigras, etc. For this reason, there is no routine in Amber to carry out this "calibration" function. You will need some program to construct files with lines like the following:
23 ALA HA 52 VAL H 3.8 # upper boundor
23 ALA HA 52 VAL H 2.7 3.8 # upper and lower boundAt this point, you can use the program "makeDIST_RST" to construct the actual sander input.
Dave Case
One route would be to integrate the volumes to intensities using SPARKY then complete matrix relaxation using CORMA/MARDIGRAS. Using RANDMARDI, (see H. Liu, J Biomol NMR. 6(4), 390-402.(1995)) you can get upper and lower bounds for distance restraints from NOE intensities.
David Konerding
I am using SANDER to refine the structure of a protein using NMR
derived restraints. For distance restraints involving equivalent
and nonstereospecifically assigned protons, I incorporate the
You do have to make corrections to the distance bounds, usually assuming
a "worst-case" geometry: i.e. to find the
I don't know that this is well-described in the literature (although it
probably is and I have missed it). You can see how AMBER does it by
looking at the "rm6" routine in "makeDIST_RST.c" (in the version 4.1
distribtuion in src/nmr_aux/prepare_input). Note that SANDER does not do
this sort of correction automatically: you need to run makeDIST_RST or
some other equivalent algorithm to get the "corrected" distance bounds.
[Also note that in most cases, the corrections are very modest: they increase
the bound by a few tenths of an Angstrom, generally by less than the uncertainty
in the bound itself.]
Dave Case
... do you know how I could get violations of the covalent geometry (bonds,
angles) in Angstroms and degrees rather than in terms of an Energy
... your violation list (made by the LISTOUT=POUT command)
should end with lines giving "RMS deviation from ideal bonds" and
"RMS deviation from ideal angles:", giving results in Angstroms and degrees.
Dave Case