Hi Jiamu,
I think the glycoside linkages are specified in the
generate.inp file. The text I list in the end of this email is
taken from my generate.inp for a structure with (man)3Gn (the
tri-mannose core plus a 1.3 arm GlcNAc, not the two core GlcNAc):
(GlcNAc)-b12-(Man)-a13-(Man)-a16-(Man). The
numbering is 4-3-2-1 in the same order.
The "C" in segid means they are 4 residues in the
"C" chain. And the sugar giving reducing end is the "-", or, the
"carbo_i".
I think the N-linkage between a GlcNAc and an Asn
is the same thing - but I've never really tried. However the default
generate.inp seems to already have two N-linked entrys (the "B1N"), you just
need to specify the residues and change the "false" to "true".
I did mine some time ago. Not sure if that is
all you need to do. Please let know if it works.
{=========================== 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="A16";
{===>} carbo_i_segid_1="C";
carbo_i_resid_1=1;
{===>} carbo_j_segid_1="C"; carbo_j_resid_1=2;
{+ choice: true false +}
{===>} carbo_use_2=true;
{===>}
carbo_patch_2="A13";
{===>} carbo_i_segid_2="C";
carbo_i_resid_2=3;
{===>} carbo_j_segid_2="C"; carbo_j_resid_2=2;
{+ choice: true false +}
{===>} carbo_use_3=true;
{===>}
carbo_patch_3="B12";
{===>} carbo_i_segid_3="C";
carbo_i_resid_3=4;
{===>} carbo_j_segid_3="C"; carbo_j_resid_3=3;
{========================= generate parameters
=============================}