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:

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--
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