Hello Woonghee--

> 
>  
> 
> What will be the easiest way to use Serine-CoA with Xplor-NIH? I guess
> genLigand.py is not suitable for this.
> 
>  

Unless you can find top/par values someone else used, I suspect it
will be easiest to use solution #1 from 

  https://nmr.cit.nih.gov/xplor-nih/faq.html#node0150.txt

to generate topology and parameter values for CoA, and then write a
little patch to attach it your protein. The required parameters for
the patch could be deduced from analogous structures.

I can help if need be.

best regards--
Charles

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