AMBER Archive (2003)

Subject: AMBER: Carbohydrate connectivity

From: Bimo Ario Tejo (bimo7_at_linuxmail.org)
Date: Thu Dec 11 2003 - 09:14:05 CST

Dear Amber users,

I'm trying to connect my protein with a sugar group. In PDB input
file, I put the sugar group after C-terminal residue of the protein:

...
ATOM 4019 CB VAL 520 59.503 65.879 -19.234 1.00 17.41
ATOM 4020 CG1 VAL 520 58.356 64.987 -18.802 1.00 14.33
ATOM 4021 CG2 VAL 520 60.675 65.007 -19.677 1.00 14.83
ATOM 4022 OXT VAL 520 60.721 67.545 -21.929 1.00 17.00
TER 4023 VAL 520
HETATM 4024 C1 4NN 990 54.019 65.786 -2.071 1.00 27.09
HETATM 4025 C2 4NN 990 53.098 67.012 -2.129 1.00 29.55
HETATM 4026 C3 4NN 990 53.671 68.182 -2.907 1.00 28.87
HETATM 4027 C4 4NN 990 55.155 68.370 -2.626 1.00 26.39
HETATM 4028 C5 4NN 990 55.908 67.077 -2.730 1.00 24.89
HETATM 4029 C6 4NN 990 57.387 67.254 -2.491 1.00 24.40
...

Th sugar group should be attached with atom ND2 of residue 314
(non-terminal residue), so I create a bond using xleap:

bond lip.314.ND2 lib.10521.C1 (leap "renumbers" 990 as 10521)

However, after I save the coordinate using "savepdb", a new
bond has been created between C-terminal residue (Val-520) with C1
atom of sugar group. It seems that "savepdb" reads the
sugar group as the next residue after Val-521 (which is not
right...).

Anyone has an experience how to connect a sugar group to non-terminal
residues of the protein?

Thank you and best wishes,
Bimo 

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