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Hello Linda-- > > I have used a spin label as a paramagnetic relaxation enhancer to > obtain distance constraints. I found the instructions for > incorporating the CYSP residue and all worked fine. However, in every > structure calculation I find that the nitroxide side chain is in a > completely extended conformation. ALL dihedrals are 180. For MTSL > X1=-60, X2=-60 and X3(CB-1SG-2SG-CL1) =+/-90 for at least a start > (these are from many crystal structures from the Hubbell group) Looking at cysp.top, I see only one dihedral angle defined- this needs to be fixed, in the absence of other information. Note that the DIHE term is normally not used in Xplor-NIH calculations- the RAMA term is preferred. However, the RAMA database will have no entries for MTSL, so DIHE will have to be used- probably with a constraint interaction statement. Do note that protocol.addUnkownAtoms() does invoke the DIHE term [ protocol.fixupCovalentGeom() does not ]. > > The cysp.top file refers to the sulfurs as SG1 and SG2 > I don't think there's a conflict with disulfides, other than both CYSP and CYS specify that the sulfur atom type to be S. So- please add the dihedral definitions to cysp.top, and the values to cysp.par, and contact me if you need further help with this. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFFUKSgPK2zrJwS/lYRAjhgAJ9GSgyFe7ZvIgcuhYafu2+NLcXvVQCfRGe0 2goADpIaPPtDmJEnIbKbYio= =+3NL -----END PGP SIGNATURE-----
