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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