Hello Sina--
>
> I am a new user of XPLOR-NIH. I am a little bit confused how to proceed.
> Is there any document to explain step by step simulation of a protein ?
>
What are you trying to accomplish? There are examples of multiple
types of calculations in the eginput subdirectory found in the Xplor-NIH
distribution. A step-by-step walk-through of some of these examples
can be found in
http://nmr.cit.nih.gov/xplor-nih/xplor-nih-tutorial.tgz
best regards--
Charles
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