I have recently been toying with certain restraints in my .rsr files,
and I have a couple questions. Can someone elaborate on the effect of
restraints which contain eight atoms and a multiple of six parameters
(I've seen 6, 12, 18, 24, and 30), and the restraints which contain 4
atoms and 28 parameters? What exactly are these parameters? Also, is
there an easy way to pick out the psi and phi restraints out of the
general dihedral restraints? Thanks in advance!
See http://salilab.org/modeller/9v1/manual/node382.html for a
description of the restraints file format. The second column (restraint
form) is the one you're probably interested in (it will be 9 for
multi-binormal (phi/psi) restraints). There is a multiple of six
parameters for each of these because there are six parameters for each
well in the function (weight, 2 means, 2 stdevs, and a correlation; see
http://salilab.org/modeller/9v1/manual/node91.html).
The other restraints you mention are almost certainly cubic spline
restraints (form 10). These are used because it is more efficient to
evaluate a cubic spline than a multiple Gaussian.