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In your generate.inp file that generates the input pdb and mtf files for 
cns there is a section called carbohydrate links which you can use to 
define the links... see below for an example of a beta link between the 
C1 and Asn N and a beta link between O4 and C1 of the next sugar. Then 
just make sure in your refine.inp file you read in the 
carbohydrate.param and carbohydrate.top files. Hope that helps.
Cheers
Craig

{=========================== carbohydrate links  
===========================}

{* Select pairs of residues that are linked *}
{* First entry is the name of the patch residue. *}
{* Second and third entries are the resid and segid for the atoms
   referenced by "-" in the patch. *}
{* Fourth and fifth entries are the resid and segid for the atoms
   referenced by "+" in the patch *}
{+ table: rows=6 numbered
          cols=6 "use" "patch name" "segid -" "resid -" "segid +" "resid 
+" +}

{+ choice: true false +}
{===>} carbo_use_1=true;
{===>} carbo_patch_1="B1N";
{===>} carbo_i_segid_1="B"; carbo_i_resid_1=901;
{===>} carbo_j_segid_1="B"; carbo_j_resid_1=131;

{+ choice: true false +}
{===>} carbo_use_2=true;
{===>} carbo_patch_2="B14";
{===>} carbo_i_segid_2="B"; carbo_i_resid_2=902;
{===>} carbo_j_segid_2="B"; carbo_j_resid_2=901;

Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630



Jiamu Du wrote:
> Dear All,
> Thank you for your previous response. I have built a 3-mer 
> oligosaccharides in the electron density by using coot. I prefer to 
> refine my structure in CNS due the resolution is only 2.6 Ang. I found 
> there are only topology and parameter files for carbohydrate in CNS 
> but no linkage file for carbohydrate. So CNS could recognize the sugar 
> molecules individually, but can not recognize the linkage between 
> them. When I refine it in CNS, a oxygen will be added beyond C1 of NAG.
> Is there anyone who has the linkage file for carbohydrate of CNS? Or 
> is there any other methods to deal with this situation?
>
> Thanks.