Hi Mi-Kyung,
Ideally, you would want your residues to be listed sequentially from the
number 1. Residue numbers that include letters are not standard PDB
format. I suspect this is your main problem.
It also appears that your residue names are off. Should
residue GLC only have one atom (O4)?
Hope this helps.
Rhonda A. Torres
The Scripps Research Institute
Department of Molecular Biology
10550 N. Torrey Pines Rd. TPC 15
La Jolla, CA 92037
email: torres.scripps.edu
phone: (858) 784-9781
fax: (858) 784-8896
On Fri, 8 Aug 2003, Mi-Kyung Seo wrote:
> Hello Amber users,
>
> I loaded pdb file made by Insight in Leap (Amber7.0) and use
> "bondByDistance" command to put in bonds using default criteria.
> However, some bonds are disconnected and structure is broken.
> Is pdb file made by Insight different from pdb format which can be loaded in
> leap?
>
> Here is the pdb file. (two disaccharides and likage between two)
> -----------------------------------------------------------------------------------------------
> ATOM 1 C1 GAL 1190 28.904 65.462 3.518 1.00 0.00
> ATOM 2 C2 GAL 1190 28.675 65.200 5.000 1.00 0.00
> ATOM 3 C3 GAL 1190 29.595 66.052 5.877 1.00 0.00
> ATOM 4 C4 GAL 1190 31.048 65.885 5.447 1.00 0.00
> ATOM 5 C5 GAL 1190 31.161 66.164 3.941 1.00 0.00
> ATOM 6 C6 GAL 1190 32.551 66.036 3.345 1.00 0.00
> ATOM 7 O2 GAL 1190 27.330 65.495 5.311 1.00 0.00
> ATOM 8 O3 GAL 1190 29.454 65.691 7.255 1.00 0.00
> ATOM 9 O4 GAL 1190 31.495 64.580 5.759 1.00 0.00
> ATOM 10 O5 GAL 1190 30.283 65.299 3.200 1.00 0.00
> ATOM 11 O6 GAL 1190 33.084 64.738 3.523 1.00 0.00
> ATOM 12 H1 GAL 1190 28.319 64.763 2.920 1.00 0.00
> ATOM 13 H2 GAL 1190 28.860 64.158 5.261 1.00 0.00
> ATOM 14 H3 GAL 1190 29.331 67.106 5.796 1.00 0.00
> ATOM 15 H4 GAL 1190 31.667 66.590 6.002 1.00 0.00
> ATOM 16 H5 GAL 1190 30.830 67.187 3.765 1.00 0.00
> ATOM 17 1H6 GAL 1190 33.254 66.733 3.801 1.00 0.00
> ATOM 18 2H6 GAL 1190 32.554 66.236 2.274 1.00 0.00
> ATOM 19 HO2 GAL 1190 27.205 66.516 5.364 1.00 0.00
> ATOM 20 HO3 GAL 1190 29.175 66.519 7.801 1.00 0.00
> ATOM 21 HO4 GAL 1190 30.707 64.025 6.124 1.00 0.00
> ATOM 22 H6 GAL 1190 32.322 64.081 3.747 1.00 0.00
> ATOM 23 C1 GAL 1191 26.714 69.474 1.875 1.00 0.00
> ATOM 24 C2 GAL 1191 28.199 69.483 2.217 1.00 0.00
> ATOM 25 C3 GAL 1191 28.887 68.389 1.419 1.00 0.00
> ATOM 26 C4 GAL 1191 28.252 67.035 1.763 1.00 0.00
> ATOM 27 C5 GAL 1191 26.772 67.123 1.405 1.00 0.00
> ATOM 28 C6 GAL 1191 25.990 65.867 1.715 1.00 0.00
> ATOM 29 O2 GAL 1191 28.766 70.743 1.890 1.00 0.00
> ATOM 30 O3 GAL 1191 30.282 68.385 1.687 1.00 0.00
> ATOM 31 O4 GAL 1191 28.411 66.736 3.177 1.00 0.00
> ATOM 32 O5 GAL 1191 26.147 68.185 2.146 1.00 0.00
> ATOM 33 O6 GAL 1191 24.629 66.012 1.331 1.00 0.00
> ATOM 34 H1 GAL 1191 26.566 69.703 0.820 1.00 0.00
> ATOM 35 H2 GAL 1191 28.311 69.299 3.286 1.00 0.00
> ATOM 36 H3 GAL 1191 28.767 68.590 0.355 1.00 0.00
> ATOM 37 H4 GAL 1191 28.762 66.276 1.170 1.00 0.00
> ATOM 38 H5 GAL 1191 26.688 67.312 0.335 1.00 0.00
> ATOM 39 1H6 GAL 1191 26.019 65.646 2.782 1.00 0.00
> ATOM 40 2H6 GAL 1191 26.403 65.011 1.181 1.00 0.00
> ATOM 41 HO3 GAL 1191 30.617 69.354 1.781 1.00 0.00
> ATOM 42 H6 GAL 1191 24.399 67.012 1.252 1.00 0.00
> ATOM 43 O4 GLC 1192 26.039 70.405 2.653 1.00 0.00
> ATOM 44 C1 METH 1 26.710 71.664 2.580 1.00 0.00
> ATOM 45 1H1 METH 1 26.189 72.382 3.180 1.00 0.00
> ATOM 46 2H1 METH 1 26.734 71.998 1.563 1.00 0.00
> ATOM 47 3H1 METH 1 27.711 71.555 2.941 1.00 0.00
> ATOM 48 C1 GAL 1170 40.006 67.891 -2.540 1.00 0.00
> ATOM 49 C2 GAL 1170 41.506 67.861 -2.857 1.00 0.00
> ATOM 50 C3 GAL 1170 41.786 68.520 -4.188 1.00 0.00
> ATOM 51 C4 GAL 1170 40.958 67.859 -5.273 1.00 0.00
> ATOM 52 C5 GAL 1170 39.471 67.852 -4.900 1.00 0.00
> ATOM 53 C6 GAL 1170 38.665 67.033 -5.871 1.00 0.00
> ATOM 54 O2 GAL 1170 42.258 68.522 -1.844 1.00 0.00
> ATOM 55 O3 GAL 1170 43.172 68.387 -4.484 1.00 0.00
> ATOM 56 O4 GAL 1170 41.417 66.534 -5.488 1.00 0.00
> ATOM 57 O5 GAL 1170 39.249 67.289 -3.590 1.00 0.00
> ATOM 58 O6 GAL 1170 37.282 67.143 -5.603 1.00 0.00
> ATOM 59 H1 GAL 1170 39.791 67.349 -1.619 1.00 0.00
> ATOM 60 H2 GAL 1170 41.872 66.835 -2.903 1.00 0.00
> ATOM 61 H3 GAL 1170 41.530 69.578 -4.138 1.00 0.00
> ATOM 62 H4 GAL 1170 41.065 68.387 -6.221 1.00 0.00
> ATOM 63 H5 GAL 1170 39.057 68.860 -4.899 1.00 0.00
> ATOM 64 1H6 GAL 1170 38.934 65.978 -5.812 1.00 0.00
> ATOM 65 2H6 GAL 1170 38.834 67.362 -6.896 1.00 0.00
> ATOM 66 HO2 GAL 1170 42.891 69.209 -2.278 1.00 0.00
> ATOM 67 HO3 GAL 1170 43.417 69.004 -5.272 1.00 0.00
> ATOM 68 HO4 GAL 1170 40.622 65.931 -5.743 1.00 0.00
> ATOM 69 H6 GAL 1170 37.022 68.137 -5.545 1.00 0.00
> ATOM 70 C1 GAL 1171 38.522 72.150 -0.740 1.00 0.00
> ATOM 71 C2 GAL 1171 37.884 71.735 -2.090 1.00 0.00
> ATOM 72 C3 GAL 1171 37.390 70.277 -2.079 1.00 0.00
> ATOM 73 C4 GAL 1171 38.412 69.320 -1.437 1.00 0.00
> ATOM 74 C5 GAL 1171 38.802 69.887 -0.090 1.00 0.00
> ATOM 75 C6 GAL 1171 39.740 69.014 0.726 1.00 0.00
> ATOM 76 O2 GAL 1171 36.762 72.574 -2.362 1.00 0.00
> ATOM 77 O3 GAL 1171 37.090 69.863 -3.405 1.00 0.00
> ATOM 78 O4 GAL 1171 39.592 69.201 -2.261 1.00 0.00
> ATOM 79 O5 GAL 1171 39.442 71.154 -0.289 1.00 0.00
> ATOM 80 O6 GAL 1171 39.515 69.191 2.124 1.00 0.00
> ATOM 81 H1 GAL 1171 37.756 72.278 0.025 1.00 0.00
> ATOM 82 H2 GAL 1171 38.584 71.818 -2.921 1.00 0.00
> ATOM 83 H3 GAL 1171 36.462 70.160 -1.520 1.00 0.00
> ATOM 84 H4 GAL 1171 37.938 68.345 -1.326 1.00 0.00
> ATOM 85 H5 GAL 1171 37.894 70.026 0.496 1.00 0.00
> ATOM 86 1H6 GAL 1171 40.782 69.261 0.519 1.00 0.00
> ATOM 87 2H6 GAL 1171 39.593 67.959 0.493 1.00 0.00
> ATOM 88 HO3 GAL 1171 36.735 70.665 -3.944 1.00 0.00
> ATOM 89 H6 GAL 1171 39.582 70.191 2.359 1.00 0.00
> ATOM 90 O4 GLC 1172 39.216 73.352 -0.876 1.00 0.00
> ATOM 91 C1 METH 1B 40.614 73.118 -0.697 1.00 0.00
> ATOM 92 1H1 METH 1B 41.147 74.041 -0.802 1.00 0.00
> ATOM 93 2H1 METH 1B 40.788 72.717 0.279 1.00 0.00
> ATOM 94 3H1 METH 1B 40.957 72.422 -1.434 1.00 0.00
> ATOM 95 N1 AMIN 1D 30.468 74.226 -0.969 1.00 0.00
> ATOM 96 H1 AMIN 1D 29.479 74.221 -0.700 1.00 0.00
> ATOM 97 C1 PROP 1E 31.086 75.193 -1.909 1.00 0.00
> ATOM 98 C3 PROP 1E 31.399 74.578 -3.295 1.00 0.00
> ATOM 99 1H1 PROP 1E 30.426 76.072 -2.036 1.00 0.00
> ATOM 100 2H1 PROP 1E 32.009 75.608 -1.450 1.00 0.00
> ATOM 101 1H3 PROP 1E 30.481 74.546 -3.912 1.00 0.00
> ATOM 102 2H3 PROP 1E 31.697 73.515 -3.184 1.00 0.00
> ATOM 103 C1 ETHL 1I 35.608 72.838 -1.519 1.00 0.00
> ATOM 104 C2 ETHL 1I 35.065 74.214 -1.924 1.00 0.00
> ATOM 105 3H1 ETHL 1I 35.852 72.859 -0.445 1.00 0.00
> ATOM 106 2H1 ETHL 1I 34.837 72.054 -1.643 1.00 0.00
> ATOM 107 1H2 ETHL 1I 34.590 74.700 -1.051 1.00 0.00
> ATOM 108 2H2 ETHL 1I 35.901 74.879 -2.226 1.00 0.00
> ATOM 109 OH OHH 1H 34.076 74.064 -2.969 1.00 0.00
> ATOM 110 C1 ALHD 1G 33.767 75.179 -3.741 1.00 0.00
> ATOM 111 O2 ALHD 1G 34.577 75.995 -4.172 1.00 0.00
> ATOM 112 N1 AMIN 1F 32.466 75.335 -4.002 1.00 0.00
> ATOM 113 H1 AMIN 1F 32.309 76.168 -4.577 1.00 0.00
> ATOM 114 C1 ETHL 1K 30.052 71.157 2.482 1.00 0.00
> ATOM 115 C2 ETHL 1K 31.015 71.589 1.375 1.00 0.00
> ATOM 116 1H1 ETHL 1K 30.499 70.382 3.136 1.00 0.00
> ATOM 117 2H1 ETHL 1K 29.881 72.021 3.153 1.00 0.00
> ATOM 118 1H2 ETHL 1K 31.970 71.926 1.826 1.00 0.00
> ATOM 119 2H2 ETHL 1K 31.264 70.740 0.709 1.00 0.00
> ATOM 120 OH OHH 1J 30.399 72.651 0.604 1.00 0.00
> ATOM 121 C1 ALHD 1C 31.196 73.346 -0.285 1.00 0.00
> ATOM 122 O2 ALHD 1C 32.413 73.191 -0.423 1.00 0.00
> TER
> ----------------------------------------------------------------------------------
>
> Thanks.
> Mikyung
>
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Received on Fri Aug 08 2003 - 00:53:00 PDT
