Error during run on Prodigy server


#1

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


#2

Is this the complete file? I assume you verified that the chains you specified as Interactor exist?
Are there non canonical amino acids in the file not labelled as HETATM?

Unfortunately there is no real error message, so troubleshooting without the. actual input is difficult.

Best

Joerg


#3

Oh, I came up with sharing the file) I haven’t understood how to attach file to the topic, so it’s here: pdb file

Thank you very much for your help!

Dana


#4

Hi,

thanks for the file. Unfortunately after briefly looking into the matter, I can’t really tell what exactly causes the issue other than that it fails in the freesasa step. If that is acceptable, I would suggest refining the complex with Haddock and see if the problem persists with the refined complex. Otherwise I can try to track down the issue at a later point.

Best

Joerg


#5

Hi Dana,

I looked again at your input and found the issue. Basically if you’d run the standalone freesasa on your protein it will notify you that it doesn’t recognize the Atoms CD of ILE and OT1 and OT2 of 2 VAL residues. If you “fix” the naming (CD to CD1, OT1 to O, and OT2 to OXT) prodigy runs just fine.

Please apologise the inconvenience. We will try to add a more helpful error message to the server.

Best

Joerg