Hello Xuehui-- > > I am trying to solve the complex structure of a peptide and a > beta-D-glucose. Is there a step-by-step protocol to follow?
Probably the most difficult aspect will be generating the sugar PSF. This reference may help: https://doi.org/10.1371/journal.pone.0189700 Distributed with Xplor-NIH there is toppar/toph3.cho, but it would be nice to distribute the updated parameters with Xplor-NIH, as they are certainly an improvement, and most likely more complete. > > I've searched for days and found nothing and I also tried the Gmane > but it told me 'server not found'. Unfortunately, gmane appears to be dead, and I need to find a different solution. I apologize. > > I've tested the determination process of the peptide part with Xplor > and it's ok. What should I do with the sugar? > Once you have a PSF, you can use a standard docking protocol, an example of which can be found in eginput/diffTens/dock/dock.py in the Xplor-NIH distribution. best regards-- Charles _______________________________________________ Xplor-nih mailing list Xplorfirstname.lastname@example.org https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih