Hello Jelena-- > > I am doing water refinement (using Xplor 2.46) for a small metalloprotein, > after > structure calculation using metal restraints in CYANA. > In my protein, I have the metal cluster which topology I "freeze" in the > wrefine.py script by fixing metals and binding atoms.
Is this accomplished using the rigidRegions argument to waterRefineTools.refine? > The problem I am experiencing is that for certain models I get extremely large > total energies even though all the models are very similar. > For example: > XplorPot VDW 17765.82(80021.66) 463.3( 80.3) > > Powell::step: irregular exit: Line search abandoned: gradient may be incorrect > *-- POWELL ------ step= 1 --- stepsize= 0.01000 --- energy evals= 5 > -* > | E(poten)=389918.3302198 grad= 30044.6033617 ANGL= > 1619.5106059 | > | BOND= 6321.6578947 CDIH= 1.0494587 DIHE= > 1028.5803754 | > | ELEC=-11596.8057242 HARM= 0.0000000 IMPR= > 132.7689804 | > | VDW=392361.9271258 noe= 49.6415031 > | > *------------------------------------------------------------------------------* It's pretty clear that something is causing problems with the VDW term. What parameters are you using for the metal ion? best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
