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Prodrg does give weird atom names...And if they conflict with heavy
atoms, then as you've found it can cause problems. The general
workaround that I have used is to draw the ligand, and submit that to
prodrg.
I bet you can instruct PRODRG to give sensible atom names if a you would
supply a PDB file with proper atoms names.
If you want to rename atoms in your ligand check out eLBOW (see link below)
I am trying to do my refinement together with my ligand using CNS. I used
the HIC-up server to generate .top and .par files using the .pdb of my
ligand. Surprisingly, the server returned those two files with a lot
of the
eLBOW spits out a CIF file that phenix.refine, REFMAC and COOT can
handle. CNS style top and par file are not supported unfortunately.
Check out http://www.phenix-online.org/phenix_wiki/eLBOW
HTH
Peter
