Hello Xu-- > > 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?
I don't believe anything special is required, but something needs to be fixed. Could you please send the script and log file? [You can send these to me privately, if you wish.] best regards-- Charles _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
