Dear Hailiang
There are several protein-sugar and sugar-sugar link defined in the standard
refmac library.
You may try running refmac with the default options with the input pdb file in
which
- sugar residues included,
- no LINK record are specified.
If all required links are in the refmac's library, the refinement will work,
and the output PDB will contain the LINK records, e.g.
...
LINK C1 NAG A1539 ND2 ASN A 341 NAG-ASN
LINK NAG A1539 NAG A1540 BETA1-4
MODRES NAG A 1539 NAG-b-D RENAME
MODRES NAG A 1540 NAG-b-D RENAME
...
In the log file you will see:
...
WARNING : link: NAG<-->NAG is without link_id
link will be created with covalent bond only. Bond= 1.430
...
WARNING : link:NAG-ASN is found dist = 1.427 ideal_dist= 1.439
ch:AA res: 341 ASN at:ND2 .->Aj res:1539 NAG at:C1
.
....
WARNING : link:BETA1-4 is found dist = 1.430 ideal_dist= 1.439
ch:Aj res:1539 NAG at:O4 .->Ak res:1540 NAG at:C1
.
...
The last two warnings actually mean that everything is fine.
Ignore the first warning, as it is overridden by the third one.
All the best
Andrey
