AMBER Archive (2006)

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

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Oct 04 2006 - 10:41:11 CDT

Sorry I find I made a mistake. In fact one residue is
ASN and the other residue is ASN. I home the one who
is responsible for the e-mail delete my previous
e-mail atom nomination in the PDB file produced by
Amber.

Best regards.

Fenghui Fan

--- Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:

> 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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