Hello Sabine--
> > I have taken over a project involving a complex of a protein with a peptide > with sulfated tyrosine. > I have a few questions. > I noticed, that the masses for several of the atoms of the modified tyrosine > were missing from the topology file. I have added them now, but what are the > consequences of missing masses for the structure calculations? > With the refine.py script I am getting errors for duplicated entries like > these > %RTFRDR-ERR: duplicate (P-)RESIdue name CIPP > %PARRDR-ERROR: duplication of bond C C > If you are replacing the default set of protein topology and parameter files, you should replace > protocol.initTopology(["data/topallhdgntccr5_M.pro"])#["protein","data/tys.pro > "]) > protocol.initParams(["data/parallhdgntccr5_SA.pro"])#,"data/tys.par"]) with import protocol protocol.topology['protein'] = "data/topallhdgntccr5_M.pro" protocol.parameters['protein'] = "data/parallhdgntccr5_SA.pro" You might want to specify an atom selection argument to fixupCovalentGeom: protocol.fixupCovalentGeom(sel="resid A:B",maxIters=100,useVDW=1) because it can cause unwanted changes to regions in the selection, which defaults to all atoms. Regarding the nonbonded violations: how are the other restraints satisfied? thanks-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
