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.
