Hi Ramon, Looks like your contraints fix statements are the problem. By fixing the entire SANI "molecule," you've forced your structure to do all the overall rotations necessary for RDC agreement. But by fixing parts of your structure as well, you've prevented that.
Change the first constraints fix selection to (segid SANI and resid 500 and name OO), and get rid of the selections for parts of your protein, and you should be all right. But note that you'd be better off using a more modern script, like xplor/eginput/gb1_rdc/refine.py to do this. Hope this helps. --JK On Mar 3, 2008, at 5:12 AM, R.M. van der Werf wrote: > Hi, > > I am trying to do a global RDC refinement, but the molecule appears to > move very little, or not at all. > > My script goes as follows (Temperature = 300K over entire script) > > 1. Read structure, parameters, restraints (NOE, RDCs, dihedrals) > 2. Introduce alignment tensor (pseudoatoms) > 3. fix helices: > constraint fix=((segid SANI and resid 500) > or (segid EDHB and resid 1:5) or (segid EDHB and resid 33:37) or > (segid EDHB and resid 14:29)) end > > My structure contains 37 residues, RDCs need to be refined for the > residues which are not fixed. > > 4. 4000 verlet dynamic steps of 0.0005 ps with the > flags bonds angle impr vdw noe cdih plan sani > 5. Loop of verlet dynamics in which in every loop step the NOE and > cdih > force is increased > 6. 20000 verlet dynamic steps of 0.0005 ps, at 'high' force for NOE > and cdih > 7. powell minimisation of 10000 steps > > Any ideas are welcome. > Increasing the timesteps moves the final structures to a higher energy > level (and thus not ending up in an energetic minimum). > Is another temperature needed ? > > Kind regards, > Ramon > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
