Hello Mark-- > > we want to refine and do a water refinement of a protein with a > bound Ca2+ ligand. I have done this for a Zn-finger protein. Do we > have to define a patch in the same way? Do you have an example? >
To use the default Xplor-NIH topology/parameters, there are patches named DCA2 and ECA2 for ligating Ca+2 to the sidechains of ASP and GLU, respectively. If you have a well-defined calcium center geometry, a specific patch can be created. These require generating a PSF, as in the zinc cast. For something looser, distance restraints can be used, possibly not requiring a PSF. For water refinement a few extra parameters are likely needed. Please let me know if I can help. 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
