Hi Ralf, This doesn't work. I removed all the H atoms from the pdb file and got the same error. Jianghai +++++++++++++++++++++++++++++++ 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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb