AMBER Archive (2006)

Subject: AMBER: atom nomination in the PDB file produced by Amber

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Oct 04 2006 - 10:37:45 CDT

Dear all,

Recently I got a pdb file from the sander rst file. In
the PDB file it contains residue ASN70 and RESIDUE
ASN75. However in the PDB file it specifies that:

ATOM 1056 N GLN 70 22.753 32.707 48.598
ATOM 1057 H GLN 70 23.379 33.243 49.182
ATOM 1058 CA GLN 70 23.205 31.336 48.365
ATOM 1059 HA GLN 70 22.525 30.849 47.667
ATOM 1060 CB GLN 70 24.723 31.257 47.760
ATOM 1061 2HB GLN 70 24.888 30.214 47.490
ATOM 1062 3HB GLN 70 24.779 31.777 46.804
ATOM 1063 CG GLN 70 25.753 31.826 48.798
ATOM 1064 2HG GLN 70 25.237 32.334 49.613
ATOM 1065 3HG GLN 70 26.364 31.025 49.214
ATOM 1066 CD GLN 70 26.744 32.784 48.030
ATOM 1067 OE1 GLN 70 26.556 33.966 47.863
ATOM 1068 NE2 GLN 70 27.866 32.237 47.605
ATOM 1069 1HE2 GLN 70 28.395 32.888 47.042
ATOM 1070 2HE2 GLN 70 28.099 31.273 47.795
ATOM 1071 C GLN 70 23.049 30.398 49.642
ATOM 1072 O GLN 70 22.949 29.203 49.495

ATOM 1137 N ASN 75 20.366 25.019 50.937
ATOM 1138 H ASN 75 20.107 25.947 50.635
ATOM 1139 CA ASN 75 19.521 24.329 51.915
ATOM 1140 HA ASN 75 19.857 23.293 51.922
ATOM 1141 CB ASN 75 19.898 24.860 53.334
ATOM 1142 2HB ASN 75 19.720 25.936 53.356
ATOM 1143 3HB ASN 75 19.209 24.372 54.023
ATOM 1144 CG ASN 75 21.280 24.579 53.781
ATOM 1145 OD1 ASN 75 21.599 23.557 54.316
ATOM 1146 ND2 ASN 75 22.218 25.497 53.627
ATOM 1147 1HD2 ASN 75 23.144 25.161 53.853
ATOM 1148 2HD2 ASN 75 22.139 26.338 53.075
ATOM 1149 C ASN 75 18.021 24.249 51.547
ATOM 1150 O ASN 75 17.237 23.729 52.300

You will find that: 1. The 2 same ASN residues has
different atom numbers specified. 2. The same 2 ASN
residues has different nomination on the same atom
(for example ND2 and NE2).

Will you please tell me why this can occur?

Best regards.

Fenghui Fan

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