Hello, I'm in Jim Prestegard's lab and we're currently trying to do low-temperature SA on a homology model using our experimental restraints. I have a few (~100) noes, dihedral and H-bond restraints and a whole suite of RDCs. Here's what I am confused about:
1)I have been reading the RDCs in as different classes (NH, CAHA, etc) but I am not sure what to do about Da and Rh- should they be the same and come from the entire data set or from the individual RDC types? What about HH? I have seen an example file that uses Dn which is 0.48*Da but I don't know where that came from. How do I handle bond lengths in the >1 bond couplings? 2) Force constants- I have read they should be scaled according to NH couplings but I am not sure what that means. I am currently starting at 0.01 for NH and increasing to 1.0 during the cooling. Any suggestions as to what the others should be? 3) HH couplings- both intra and inter-residue. I've been told I can't use sani for non-1 bond restraints so how do I read these in? 4) Potentials- I understand "square" uses errors and "harmonic" doesn't but I see input files where people always use square for RDCs. How do you incorporate errors for the RDCs? Thanks so much for your help! Kristen Mayer PhD
