I now know what happened. When reduce adds H atoms into the pdb file, it finds the glycosylation bonds between NAG and ASN. There are two H atoms attached to the ND2 of ASN and reduce deletes the H atom named HD21 and keeps HD22. However, in the mon_lib_list.cif, the library wants to delete the other H atom named HD22 and keep HD21. That's where this error came from. So if I change the HD22 to HD21, everything is fine. If I delete HD22, it is fine too. I have a lot of glycans and it is very tedious to manually change HD22 to HD21 or delete HD22 one by one in the pdb file. Could you please fix this? Thanks.

+++++++++++++++++++++++++++++++

Jianghai Zhu, Ph.D

CBR Institute for Biomedical Research

Department of Pathology

Harvard Medical School

200 Longwood Ave., Boston, MA 02115

Ph: 617-278-3211

Fx: 618-278-3232

+++++++++++++++++++++++++++++++

On Oct 6, 2007, at 10:40 PM, Ralf W. Grosse-Kunstleve wrote:

Hi Jianghai,

The NAG-ASN link is defined with two modifications (in mon_lib_list.cif):

NAG-ASN NAG DEL-O1 . ASN DEL-HD22 .
bond_NAG-C1_=_ASN-ND2

I haven't looked at the chemistry, but this definition suggests you
have to remove the HD22 atom. I.e. remove the corresponding ATOM
record from you PDB file. Note that

Number of atoms with unknown nonbonded energy type symbols: 1
"HD22 ASN A 15 "

is formatted exactly like in the PDB file, so you can use this
as a search pattern to find the line directly.

Ralf
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