Questions and problems

NMR topics

... 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 bound
23  ALA  HA      52 VAL H    2.7  3.8   # upper and lower bound
At 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 -1/6 effective distance using the IGR1, IGR2 and IR6 options of SANDER. My question is: What sort of distance corrections to the upper bound proton-proton distance restraints derived from the NOE cross-peaks are required in this case?. I presume that are not the same used in the case of employing pseudoatoms.

You do have to make corrections to the distance bounds, usually assuming a "worst-case" geometry: i.e. to find the -weighted distance that would just fit inside the (assumed) original bound.

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