Hello Yikan-- > > Recently, I am doing conformational sampling with Xplor-NIH. And I > got many pdbs, but when I check them I found that some pdbs have > wrong topology structures like the attachments(in the pink cycle ): > The RNA linker did not run with the right way and It went through > the helix. I have tried to pick the structures by the “total energy” > or “repel” terms, but it make no sense. Are there someone know how > to kick out these wrong structures or to void these errors in the > sampling process? Thank you!
Based on the picture and the description you have given, this sort of knotted structure must be accompanied by local clashes, and in this case coupled with disruptions of expected base hydrogen bonding. If there is no signature of the problem in the global energies, perhaps you could look for correlations of local properties- such as violated hydrogen bonds coupled with nearby clashes. what do you think? Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
