Building an NMR structure
This experiment will try to solve a structure from NMR data. The data are derived from the examples in the pdb.
While the program AMMP will be
used in the experiments, learning to use this program is not a major
point of the lessons. You will not be tested on AMMP. There are many programs
available for modeling, but despite the advertising copy they are
very similar in choice of algorithms and quality of results.
Download ammp and one or more of these files. The run files will build the molecule from NMR data. Distance data does not contain handedness information so the model will be built in either the left or right hand.
It is useful to turn on the display of the distance terms (NOEL in the ammp language). They will be green if they are "met" or red if they are not (they will all be green until the first energy minimization step).
Normally after the initial model building the structure would be further refinedby molecular dynamics.
- read the molecule (1pyc)
- read either kohonen.run, sadgeom.run, or abuild.run
- read rms.run and/or rms.left.run