I tried to calculate protein-protein binding energy using prodigy server, but obtained this error. I read rules for pdb filed and still do not understand what am I doing wrong…
I haven’t understood how to attach file to the topic. I tried all what I could imagine: with and without hydrogens, with two TER’s and with one, with blank line in the end and without, etc. I think there could be problems with atom names, but I haven’t found anywhere instructions which names are correct for Prodigy…
I will be grateful for any help
The beginning of the file is hiden
pdbfile
ATOM 1 N GLU A 1 3.917 -18.735 -65.428 0.00 0.00 N1+
ATOM 2 CA GLU A 1 2.677 -18.238 -64.861 0.00 0.00 C
ATOM 3 CB GLU A 1 1.808 -19.404 -64.318 0.00 0.00 C
ATOM 4 CG GLU A 1 0.448 -18.991 -63.683 0.00 0.00 C
ATOM 5 CD GLU A 1 -0.410 -20.140 -63.147 0.00 0.00 C
ATOM 6 OE1 GLU A 1 -1.507 -19.791 -62.638 0.00 0.00 O
ATOM 7 OE2 GLU A 1 0.005 -21.321 -63.219 0.00 0.00 O
ATOM 8 C GLU A 1 3.044 -17.251 -63.764 1.00 0.00 C
ATOM 9 O GLU A 1 4.221 -17.003 -63.500 0.00 0.00 O
ATOM 10 N ASP A 2 1.928 -16.604 -63.030 1.00 0.00 N
ATOM 11 CA ASP A 2 2.362 -15.644 -61.965 1.00 0.00 C
ATOM 12 CB ASP A 2 2.611 -16.386 -60.640 1.00 0.00 C
ATOM 13 CG ASP A 2 4.042 -16.936 -60.532 1.00 0.00 C
ATOM 14 OD1 ASP A 2 4.627 -16.895 -59.422 1.00 0.00 O
ATOM 15 OD2 ASP A 2 4.588 -17.389 -61.566 1.00 0.00 O
ATOM 16 C ASP A 2 3.638 -14.875 -62.372 1.00 0.00 C
ATOM 17 O ASP A 2 4.740 -15.209 -61.897 1.00 0.00 O
ATOM 18 N ASP A 3 3.510 -13.825 -63.196 1.00 0.00 N
ATOM 19 CA ASP A 3 2.231 -13.187 -63.568 1.00 0.00 C
ATOM 20 CB ASP A 3 1.565 -13.832 -64.799 1.00 0.00 C
ATOM 21 CG ASP A 3 0.804 -12.809 -65.670 1.00 0.00 C
ATOM 22 OD1 ASP A 3 0.731 -13.026 -66.898 1.00 0.00 O
ATOM 23 OD2 ASP A 3 0.288 -11.793 -65.158 1.00 0.00 O
ATOM 24 C ASP A 3 1.274 -13.144 -62.389 1.00 0.00 C
ATOM 25 O ASP A 3 0.669 -14.152 -62.000 1.00 0.00 O
ATOM 26 N ILE A 4 1.153 -11.972 -61.837 1.00 0.00 N
ATOM 27 CA ILE A 4 0.329 -11.873 -60.627 1.00 0.00 C
ATOM 28 CB ILE A 4 1.182 -11.980 -59.348 1.00 0.00 C
ATOM 29 CG2 ILE A 4 0.308 -11.823 -58.130 1.00 0.00 C
ATOM 30 CG1 ILE A 4 1.959 -13.296 -59.307 1.00 0.00 C
ATOM 31 CD ILE A 4 3.383 -13.164 -59.782 1.00 0.00 C
ATOM 32 C ILE A 4 -0.405 -10.535 -60.578 1.00 0.00 C
ATOM 33 O ILE A 4 0.190 -9.520 -60.227 1.00 0.00 O
ATOM 34 N ILE A 5 -1.688 -10.525 -60.922 1.00 0.00 N
ATOM 35 CA ILE A 5 -2.386 -9.260 -61.138 1.00 0.00 C
ATOM 36 CB ILE A 5 -2.427 -8.882 -62.641 1.00 0.00 C
ATOM 37 CG2 ILE A 5 -3.322 -7.666 -62.871 1.00 0.00 C
ATOM 38 CG1 ILE A 5 -1.022 -8.558 -63.145 1.00 0.00 C
ATOM 39 CD ILE A 5 -0.923 -8.462 -64.645 1.00 0.00 C
ATOM 40 C ILE A 5 -3.801 -9.244 -60.581 1.00 0.00 C
ATOM 41 O ILE A 5 -4.616 -10.105 -60.903 1.00 0.00 O
ATOM 42 N ILE A 6 -4.090 -8.241 -59.760 1.00 0.00 N
ATOM 43 CA ILE A 6 -5.402 -8.100 -59.149 1.00 0.00 C
ATOM 44 CB ILE A 6 -5.302 -8.181 -57.626 1.00 0.00 C
ATOM 45 CG2 ILE A 6 -6.644 -7.863 -56.970 1.00 0.00 C
ATOM 46 CG1 ILE A 6 -4.781 -9.569 -57.216 1.00 0.00 C
ATOM 47 CD ILE A 6 -5.741 -10.680 -57.538 1.00 0.00 C
ATOM 48 C ILE A 6 -6.024 -6.777 -59.536 1.00 0.00 C
ATOM 49 O ILE A 6 -5.414 -5.726 -59.365 1.00 0.00 O
ATOM 50 N ALA A 7 -7.231 -6.834 -60.084 1.00 0.00 N
ATOM 51 CA ALA A 7 -7.995 -5.635 -60.399 1.00 0.00 C
ATOM 52 CB ALA A 7 -9.054 -5.937 -61.461 1.00 0.00 C
ATOM 53 C ALA A 7 -8.648 -5.079 -59.133 1.00 0.00 C
ATOM 54 O ALA A 7 -9.419 -5.767 -58.473 1.00 0.00 O
ATOM 55 N THR A 8 -8.323 -3.836 -58.795 1.00 0.00 N
ATOM 56 CA THR A 8 -8.934 -3.166 -57.654 1.00 0.00 C
ATOM 57 CB THR A 8 -7.879 -2.608 -56.669 1.00 0.00 C
ATOM 58 OG1 THR A 8 -7.289 -1.423 -57.218 1.00 0.00 O
ATOM 59 CG2 THR A 8 -6.789 -3.643 -56.390 1.00 0.00 C
ATOM 60 C THR A 8 -9.790 -2.010 -58.148 1.00 0.00 C
ATOM 61 O THR A 8 -9.778 -1.669 -59.338 1.00 0.00 O
ATOM 62 N LYS A 9 -10.527 -1.404 -57.223 1.00 0.00 N
ATOM 63 CA LYS A 9 -11.356 -0.249 -57.533 1.00 0.00 C
ATOM 64 CB LYS A 9 -12.114 0.217 -56.286 1.00 0.00 C
ATOM 65 CG LYS A 9 -13.135 -0.784 -55.783 1.00 0.00 C
ATOM 66 CD LYS A 9 -14.181 -1.089 -56.850 1.00 0.00 C
ATOM 67 CE LYS A 9 -14.905 -2.409 -56.561 1.00 0.00 C
ATOM 68 NZ LYS A 9 -15.605 -2.410 -55.243 1.00 0.00 N1+
ATOM 69 C LYS A 9 -10.517 0.891 -58.110 1.00 0.00 C
ATOM 70 O LYS A 9 -10.992 1.650 -58.950 1.00 0.00 O
ATOM 71 N ASN A 10 -9.259 0.975 -57.680 1.00 0.00 N
ATOM 72 CA ASN A 10 -8.356 2.044 -58.098 1.00 0.00 C
ATOM 73 CB ASN A 10 -7.448 2.428 -56.933 1.00 0.00 C
ATOM 74 CG ASN A 10 -8.231 2.773 -55.691 1.00 0.00 C
ATOM 75 OD1 ASN A 10 -8.084 2.132 -54.649 1.00 0.00 O
ATOM 76 ND2 ASN A 10 -9.089 3.779 -55.799 1.00 0.00 N
ATOM 77 C ASN A 10 -7.518 1.759 -59.351 1.00 0.00 C
ATOM 78 O ASN A 10 -6.894 2.670 -59.906 1.00 0.00 O