Hello Silke-- > > I wanted to calculate an RNA structure and just upgraded my xplor > NIH version from 2.44 to 3.0. Thereby I realized that I get > additional warnings regarding the torsion angles. I tested then the > 'rna' example in eginput and got the same... > > setTorsions: WARNING: no angle found for > ["resid 7 and name c5'", "resid 7 and name c4'", "resid 7 and name c3'", > "resid 7 and name o3'"] > ... > > I get this warning for all sugar pucker angles (delta, nu0, nu1), > but not for the chi angles as well as the other backbone angles > (alpha, beta, gamma,...). Otherwise the calculations seem to run > fine and also the sugar puckers seem to be included as I get also > violation for them. I was wondering what does it mean and if it is a > real issue or if I can just ignore it. >
setTorsionsFromTable uses an IVM object to identify and manipulate torsion angles. If one of the torsion angle specified in your restraints is not present in the IVM object, this warning is printed. What has changed since 2.44 is that, by default, ribose ring degrees of freedom are now allow bending in addition to torsion, so they are no longer identified here (as pure torsion angles). All torsion angles are still included in the energy, though, so while the torsion angles are not set in initial randomized structure, the effect of the restraints is still present during the structure calculation. As this warning only relates to the initial structure, I think you can ignore it so long as the restraints are satisfied by the end of the calculation. best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
