c.spronk at cmbi.kun.nl
Mon Oct 21 15:51:36 CEST 2002
I would like to suggest the following useful additions to the GROMACS package related to NMR refinement:
When the dihedral angle restraints have been implemented it would be good to have a g_dihed function that prints the violations for dihedrals. A similar function would be very useful as well for the orientational restraints (orire, g_orire) (It's not clear to me how this is done currently). For the orientational restraints the following measure of fit is often used in the NMR community and would be good to have implemented:
Q = rms (D-experimental - D-calculated) / rms (D-experimental)
(Cornilescu Q-factor, Cornilescu et al. J. Am. Chem. Soc. 1998, 120, 6836-6837)
It also might be useful to have these types of restraints handled in g_energy with the -viol option.
thanks in advance!
PS I remember noticing sometime ago that g_energy -viol does not show any lower-bound violations of distance restraints. Probably a small bug.
PPS If you are interested: I'd be happy to contribute all the NMR refinement protocols that I am currently developing to the GROMACS community once they're all finished.
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