[apbs-users] Output PDB file from Nucleic acid builder does not work with PDB2PQR
Porter Hall
DEBUG INFO: PDBInputError /Users/d3y382/tmp/src/routines.py: 622
Error encountered: No heavy atoms found. You may also see this message if PDB2PQR does not have parameters for any residue in your protein.
I am not sure what is wrong with the PDB file as I have tried to make some comparisons with one that works and cannot quite figure out the issue. Does anyone have any experience running NAB outputs through PDB2PQR? Here is part of the output file for reference.
ATOM 1 HO5' G A 1 -0.423 -8.150 -2.094 1.00 0.00
ATOM 2 O5' G A 1 0.427 -7.826 -1.788 1.00 0.00
ATOM 3 C5' G A 1 1.443 -7.510 -2.756 1.00 0.00
ATOM 4 1H5' G A 1 1.100 -6.745 -3.453 1.00 0.00
ATOM 5 2H5' G A 1 1.674 -8.423 -3.305 1.00 0.00
ATOM 6 C4' G A 1 2.695 -7.020 -2.053 1.00 0.00
ATOM 7 H4' G A 1 3.574 -7.056 -2.696 1.00 0.00
ATOM 8 O4' G A 1 2.477 -5.630 -1.823 1.00 0.00
ATOM 9 C1' G A 1 2.308 -5.333 -0.452 1.00 0.00
ATOM 10 H1' G A 1 3.112 -4.686 -0.101 1.00 0.00
ATOM 11 N9 G A 1 1.098 -4.468 -0.370 1.00 0.00
ATOM 12 C8 G A 1 -0.232 -4.827 -0.384 1.00 0.00
ATOM 13 H8 G A 1 -0.509 -5.868 -0.465 1.00 0.00
ATOM 14 N7 G A 1 -1.059 -3.814 -0.295 1.00 0.00
ATOM 15 C5 G A 1 -0.218 -2.705 -0.216 1.00 0.00
ATOM 16 C6 G A 1 -0.532 -1.326 -0.103 1.00 0.00
ATOM 17 O6 G A 1 -1.635 -0.790 -0.047 1.00 0.00
ATOM 18 N1 G A 1 0.628 -0.540 -0.053 1.00 0.00
ATOM 19 H1 G A 1 0.509 0.450 0.029 1.00 0.00
ATOM 20 C2 G A 1 1.921 -1.023 -0.106 1.00 0.00
ATOM 21 N2 G A 1 2.891 -0.108 -0.043 1.00 0.00
ATOM 22 1H2 G A 1 2.778 0.893 0.027 1.00 0.00
ATOM 23 2H2 G A 1 3.839 -0.452 -0.090 1.00 0.00
ATOM 24 N3 G A 1 2.214 -2.317 -0.212 1.00 0.00
ATOM 25 C4 G A 1 1.101 -3.094 -0.261 1.00 0.00
ATOM 26 C3' G A 1 2.950 -7.607 -0.665 1.00 0.00
ATOM 27 H3' G A 1 2.586 -8.629 -0.554 1.00 0.00
ATOM 28 C2' G A 1 2.148 -6.679 0.247 1.00 0.00
ATOM 29 1H2' G A 1 1.344 -7.241 0.722 1.00 0.00
ATOM 30 2H2' G A 1 2.804 -6.267 1.014 1.00 0.00
ATOM 31 O3' G A 1 4.324 -7.545 -0.307 1.00 0.00
ATOM 32 P C A 2 4.728 -7.626 1.239 1.00 0.00
ATOM 33 O1P C A 2 6.009 -8.356 1.380 1.00 0.00
ATOM 34 O2P C A 2 3.592 -8.164 2.021 1.00 0.00
ATOM 35 O5' C A 2 4.945 -6.081 1.592 1.00 0.00
ATOM 36 C5' C A 2 5.582 -5.227 0.624 1.00 0.00
ATOM 37 1H5' C A 2 4.855 -4.809 -0.072 1.00 0.00
ATOM 38 2H5' C A 2 6.306 -5.829 0.075 1.00 0.00
ATOM 39 C4' C A 2 6.306 -4.095 1.327 1.00 0.00
ATOM 40 H4' C A 2 7.038 -3.607 0.684 1.00 0.00
ATOM 41 O4' C A 2 5.313 -3.099 1.557 1.00 0.00
ATOM 42 C1' C A 2 5.002 -2.958 2.928 1.00 0.00
ATOM 43 H1' C A 2 5.272 -1.961 3.278 1.00 0.00
ATOM 44 N1 C A 2 3.515 -2.969 3.010 1.00 0.00
ATOM 45 C6 C A 2 2.819 -4.138 2.981 1.00 0.00
ATOM 46 H6 C A 2 3.346 -5.077 2.898 1.00 0.00
ATOM 47 C5 C A 2 1.464 -4.148 3.055 1.00 0.00
ATOM 48 H5 C A 2 0.924 -5.095 3.030 1.00 0.00
ATOM 49 C4 C A 2 0.811 -2.878 3.165 1.00 0.00
ATOM 50 N4 C A 2 -0.509 -2.813 3.242 1.00 0.00
ATOM 51 1H4 C A 2 -0.930 -1.898 3.319 1.00 0.00
ATOM 52 2H4 C A 2 -1.062 -3.658 3.224 1.00 0.00
ATOM 53 N3 C A 2 1.506 -1.733 3.193 1.00 0.00
ATOM 54 C2 C A 2 2.861 -1.744 3.117 1.00 0.00
ATOM 55 O2 C A 2 3.536 -0.708 3.139 1.00 0.00
ATOM 56 C3' C A 2 6.858 -4.420 2.715 1.00 0.00
ATOM 57 H3' C A 2 7.164 -5.460 2.826 1.00 0.00
ATOM 58 C2' C A 2 5.664 -4.141 3.627 1.00 0.00
ATOM 59 1H2' C A 2 5.344 -5.069 4.102 1.00 0.00
ATOM 60 2H2' C A 2 5.952 -3.422 4.394 1.00 0.00
Thank you very much,
Porter Hall
Nathan Baker
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