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Hi-- > 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? each class has a single Da and Rh- so you need to separate each experiment into its own class. > 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. You shouldn't use the SANI term for HH experiments- use the DIPO term instead and specify type vard so that the distance dependence is used (and taken out of the expression for Da). > > 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? We use the convention that the rdc prefactor is normalized to those of NH. This prefactor consists of the gyromagnetic ratios and bond lengths. The force constants would then be multiplied by the inverse of this factor. > > 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? You need to use the DIPO term instead. See above. > 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? this error is encoded in the rdc table and the last number of the assign statement. I hope this answers your questions. As a final note, I'll make a plug for the RDC term in the Python interface- there are tools to make many of these issues simpler. However, I wouldn't look at it until we release the next version in a week or so. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQE++x/APK2zrJwS/lYRAhVfAJ9iF5I6XvBRbcjGON5rbN9snw+DRwCfR1C+ pflQqJwoa+sFHPQQXq3g5jI= =eBlH -----END PGP SIGNATURE-----
