Hi Has anyone tried the water refinement protocol with protein-ligand complexes? I know the protocol uses its own parameter and topology files for proteins, but is it OK with the inclusion of extra parameter and topology files for the ligand? I modified the wrefine.py script to read in the ligand parameter file with the initParams command and pre-generated psf files with the old XPLOR structure command. The log file indicate the files are read in OK. But it complains about missing bond, angle, improper specifications for the ligand during the dynamics stage. How do I include these parameters properly for the water refinement protocol?
Xu Wang
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