ChargeFW2
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sb-ncbr
Issue when residue numbers > 999
I see this error when processing pdb files with residue numbers into the thousands, which shifts over column placement starting at the residue number:
Input:
ATOM 16105 N GLN D 998 43.421 -12.294 -52.399 1.00 0.00 PROT N 0
ATOM 16106 H GLN D 998 42.753 -12.039 -51.685 1.00 0.00 PROT H 0
ATOM 16107 CA GLN D 998 43.531 -13.687 -52.800 1.00 0.00 PROT C 0
ATOM 16108 HA GLN D 998 44.572 -13.996 -52.704 1.00 0.00 PROT H 0
ATOM 16109 CB GLN D 998 42.668 -14.596 -51.921 1.00 0.00 PROT C 0
ATOM 16110 HB2 GLN D 998 42.994 -14.478 -50.888 1.00 0.00 PROT H 0
ATOM 16111 HB3 GLN D 998 41.631 -14.269 -51.997 1.00 0.00 PROT H 0
ATOM 16112 CG GLN D 998 42.738 -16.107 -52.280 1.00 0.00 PROT C 0
ATOM 16113 HG2 GLN D 998 42.017 -16.645 -51.665 1.00 0.00 PROT H 0
ATOM 16114 HG3 GLN D 998 42.470 -16.233 -53.329 1.00 0.00 PROT H 0
ATOM 16115 CD GLN D 998 44.120 -16.708 -52.047 1.00 0.00 PROT C 0
ATOM 16116 OE1 GLN D 998 44.916 -16.216 -51.221 1.00 0.00 PROT O 0
ATOM 16117 NE2 GLN D 998 44.433 -17.744 -52.793 1.00 0.00 PROT N 0
ATOM 16118 HE21 GLN D 998 43.767 -18.105 -53.461 1.00 0.00 PROT H 0
ATOM 16119 HE22 GLN D 998 45.340 -18.179 -52.698 1.00 0.00 PROT H 0
ATOM 16120 C GLN D 998 43.114 -13.820 -54.271 1.00 0.00 PROT C 0
ATOM 16121 O GLN D 998 43.733 -14.588 -54.959 1.00 0.00 PROT O 0
ATOM 16122 N CYS D 999 42.055 -13.130 -54.739 1.00 0.00 PROT N 0
ATOM 16123 H CYS D 999 41.485 -12.589 -54.104 1.00 0.00 PROT H 0
ATOM 16124 CA CYS D 999 41.725 -13.164 -56.189 1.00 0.00 PROT C 0
ATOM 16125 HA CYS D 999 41.494 -14.195 -56.458 1.00 0.00 PROT H 0
ATOM 16126 CB CYS D 999 40.490 -12.316 -56.469 1.00 0.00 PROT C 0
ATOM 16127 HB2 CYS D 999 40.592 -11.362 -55.952 1.00 0.00 PROT H 0
ATOM 16128 HB3 CYS D 999 40.417 -12.135 -57.541 1.00 0.00 PROT H 0
ATOM 16129 SG CYS D 999 38.962 -13.138 -55.897 1.00 0.00 PROT S 0
ATOM 16130 HG CYS D 999 38.881 -13.052 -54.566 1.00 0.00 PROT H 0
ATOM 16131 C CYS D 999 42.893 -12.688 -57.084 1.00 0.00 PROT C 0
ATOM 16132 O CYS D 999 43.214 -13.299 -58.083 1.00 0.00 PROT O 0
ATOM 16133 N ILE D1000 43.525 -11.581 -56.717 1.00 0.00 PROT N 0
ATOM 16134 H ILE D1000 43.197 -11.085 -55.900 1.00 0.00 PROT H 0
ATOM 16135 CA ILE D1000 44.675 -11.048 -57.443 1.00 0.00 PROT C 0
ATOM 16136 HA ILE D1000 44.372 -10.902 -58.480 1.00 0.00 PROT H 0
ATOM 16137 CB ILE D1000 45.031 -9.669 -56.863 1.00 0.00 PROT C 0
ATOM 16138 HB ILE D1000 45.126 -9.776 -55.782 1.00 0.00 PROT H 0
ATOM 16139 CG2 ILE D1000 46.381 -9.195 -57.407 1.00 0.00 PROT C 0
ATOM 16140 HG21 ILE D1000 46.619 -8.218 -56.988 1.00 0.00 PROT H 0
ATOM 16141 HG22 ILE D1000 46.329 -9.121 -58.493 1.00 0.00 PROT H 0
ATOM 16142 HG23 ILE D1000 47.156 -9.909 -57.128 1.00 0.00 PROT H 0
ATOM 16143 CG1 ILE D1000 43.878 -8.670 -57.141 1.00 0.00 PROT C 0
ATOM 16144 HG12 ILE D1000 43.932 -8.369 -58.187 1.00 0.00 PROT H 0
ATOM 16145 HG13 ILE D1000 42.929 -9.178 -56.973 1.00 0.00 PROT H 0
ATOM 16146 CD1 ILE D1000 43.915 -7.427 -56.291 1.00 0.00 PROT C 0
ATOM 16147 HD11 ILE D1000 43.074 -6.784 -56.550 1.00 0.00 PROT H 0
ATOM 16148 HD12 ILE D1000 44.849 -6.893 -56.469 1.00 0.00 PROT H 0
ATOM 16149 HD13 ILE D1000 43.850 -7.704 -55.239 1.00 0.00 PROT H 0
ATOM 16150 C ILE D1000 45.845 -12.055 -57.436 1.00 0.00 PROT C 0
ATOM 16151 O ILE D1000 46.413 -12.398 -58.501 1.00 0.00 PROT O 0
ATOM 16152 N LYS D1001 46.113 -12.622 -56.269 1.00 0.00 PROT N 0
ATOM 16153 H LYS D1001 45.602 -12.352 -55.440 1.00 0.00 PROT H 0
ATOM 16154 CA LYS D1001 47.138 -13.624 -56.197 1.00 0.00 PROT C 0
ATOM 16155 HA LYS D1001 48.096 -13.172 -56.454 1.00 0.00 PROT H 0
ATOM 16156 CB LYS D1001 47.197 -14.127 -54.786 1.00 0.00 PROT C 0
ATOM 16157 HB2 LYS D1001 46.312 -14.737 -54.605 1.00 0.00 PROT H 0
ATOM 16158 HB3 LYS D1001 47.173 -13.272 -54.111 1.00 0.00 PROT H 0
ATOM 16159 CG LYS D1001 48.417 -14.960 -54.465 1.00 0.00 PROT C 0
ATOM 16160 HG2 LYS D1001 48.629 -15.647 -55.284 1.00 0.00 PROT H 0
ATOM 16161 HG3 LYS D1001 49.276 -14.311 -54.294 1.00 0.00 PROT H 0
ATOM 16162 CD LYS D1001 48.094 -15.740 -53.196 1.00 0.00 PROT C 0
ATOM 16163 HD2 LYS D1001 47.247 -15.262 -52.703 1.00 0.00 PROT H 0
ATOM 16164 HD3 LYS D1001 47.813 -16.757 -53.471 1.00 0.00 PROT H 0
ATOM 16165 CE LYS D1001 49.220 -15.799 -52.239 1.00 0.00 PROT C 0
ATOM 16166 HE2 LYS D1001 48.845 -16.077 -51.254 1.00 0.00 PROT H 0
ATOM 16167 HE3 LYS D1001 49.700 -14.822 -52.182 1.00 0.00 PROT H 0
ATOM 16168 NZ LYS D1001 50.201 -16.804 -52.694 1.00 0.00 PROT N 0
ATOM 16169 HZ1 LYS D1001 51.133 -16.497 -52.454 1.00 0.00 PROT H 0
ATOM 16170 HZ2 LYS D1001 50.011 -17.688 -52.244 1.00 0.00 PROT H 0
ATOM 16171 HZ3 LYS D1001 50.131 -16.914 -53.695 1.00 0.00 PROT H 0
ATOM 16172 C LYS D1001 46.869 -14.798 -57.141 1.00 0.00 PROT C 0
ATOM 16173 O LYS D1001 47.773 -15.266 -57.875 1.00 0.00 PROT O 0
output:
ATOM 16105 N GLN D 998 43.421 -12.294 -52.399 -0.126 1.550
ATOM 16106 H GLN D 998 42.753 -12.039 -51.685 0.081 1.200
ATOM 16107 CA GLN D 998 43.531 -13.687 -52.800 0.016 1.700
ATOM 16108 HA GLN D 998 44.572 -13.996 -52.704 0.073 1.200
ATOM 16109 CB GLN D 998 42.668 -14.596 -51.921 0.006 1.700
ATOM 16110 HB2 GLN D 998 42.994 -14.478 -50.888 0.070 1.200
ATOM 16111 HB3 GLN D 998 41.631 -14.269 -51.997 0.069 1.200
ATOM 16112 CG GLN D 998 42.738 -16.107 -52.280 0.005 1.700
ATOM 16113 HG2 GLN D 998 42.017 -16.645 -51.665 0.067 1.200
ATOM 16114 HG3 GLN D 998 42.470 -16.233 -53.329 0.068 1.200
ATOM 16115 CD GLN D 998 44.120 -16.708 -52.047 0.023 1.700
ATOM 16116 OE1 GLN D 998 44.916 -16.216 -51.221 -0.254 1.520
ATOM 16117 NE2 GLN D 998 44.433 -17.744 -52.793 -0.134 1.550
ATOM 16118 HE21 GLN D 998 43.767 -18.105 -53.461 0.073 1.200
ATOM 16119 HE22 GLN D 998 45.340 -18.179 -52.698 0.074 1.200
ATOM 16120 C GLN D 998 43.114 -13.820 -54.271 0.029 1.700
ATOM 16121 O GLN D 998 43.733 -14.588 -54.959 -0.254 1.520
ATOM 16122 N CYS D 999 42.055 -13.130 -54.739 -0.128 1.550
ATOM 16123 H CYS D 999 41.485 -12.589 -54.104 0.080 1.200
ATOM 16124 CA CYS D 999 41.725 -13.164 -56.189 0.011 1.700
ATOM 16125 HA CYS D 999 41.494 -14.195 -56.458 0.068 1.200
ATOM 16126 CB CYS D 999 40.490 -12.316 -56.469 0.000 1.700
ATOM 16127 HB2 CYS D 999 40.592 -11.362 -55.952 0.064 1.200
ATOM 16128 HB3 CYS D 999 40.417 -12.135 -57.541 0.059 1.200
ATOM 16129 SG CYS D 999 38.962 -13.138 -55.897 -0.182 1.800
ATOM 16130 HG CYS D 999 38.881 -13.052 -54.566 0.073 1.200
ATOM 16131 C CYS D 999 42.893 -12.688 -57.084 0.022 1.700
ATOM 16132 O CYS D 999 43.214 -13.299 -58.083 -0.259 1.520
ATOM 16133 N ILE D 1000 43.525 -11.581 -56.717 -0.134 1.550
ATOM 16134 H ILE D 1000 43.197 -11.085 -55.900 0.073 1.200
ATOM 16135 CA ILE D 1000 44.675 -11.048 -57.443 0.004 1.700
ATOM 16136 HA ILE D 1000 44.372 -10.902 -58.480 0.061 1.200
ATOM 16137 CB ILE D 1000 45.031 -9.669 -56.863 -0.008 1.700
ATOM 16138 HB ILE D 1000 45.126 -9.776 -55.782 0.063 1.200
ATOM 16139 CG2 ILE D 1000 46.381 -9.195 -57.407 -0.014 1.700
ATOM 16140 HG21 ILE D 1000 46.619 -8.218 -56.988 0.055 1.200
ATOM 16141 HG22 ILE D 1000 46.329 -9.121 -58.493 0.054 1.200
ATOM 16142 HG23 ILE D 1000 47.156 -9.909 -57.128 0.060 1.200
ATOM 16143 CG1 ILE D 1000 43.878 -8.670 -57.141 -0.017 1.700
ATOM 16144 HG12 ILE D 1000 43.932 -8.369 -58.187 0.049 1.200
ATOM 16145 HG13 ILE D 1000 42.929 -9.178 -56.973 0.055 1.200
ATOM 16146 CD1 ILE D 1000 43.915 -7.427 -56.291 -0.021 1.700
ATOM 16147 HD11 ILE D 1000 43.074 -6.784 -56.550 0.048 1.200
ATOM 16148 HD12 ILE D 1000 44.849 -6.893 -56.469 0.051 1.200
ATOM 16149 HD13 ILE D 1000 43.850 -7.704 -55.239 0.056 1.200
ATOM 16150 C ILE D 1000 45.845 -12.055 -57.436 0.023 1.700
ATOM 16151 O ILE D 1000 46.413 -12.398 -58.501 -0.257 1.520
ATOM 16152 N LYS D 1001 46.113 -12.622 -56.269 -0.130 1.550
ATOM 16153 H LYS D 1001 45.602 -12.352 -55.440 0.078 1.200
ATOM 16154 CA LYS D 1001 47.138 -13.624 -56.197 0.012 1.700
ATOM 16155 HA LYS D 1001 48.096 -13.172 -56.454 0.069 1.200
ATOM 16156 CB LYS D 1001 47.197 -14.127 -54.786 0.001 1.700
ATOM 16157 HB2 LYS D 1001 46.312 -14.737 -54.605 0.067 1.200
ATOM 16158 HB3 LYS D 1001 47.173 -13.272 -54.111 0.066 1.200
ATOM 16159 CG LYS D 1001 48.417 -14.960 -54.465 -0.001 1.700
ATOM 16160 HG2 LYS D 1001 48.629 -15.647 -55.284 0.068 1.200
ATOM 16161 HG3 LYS D 1001 49.276 -14.311 -54.294 0.065 1.200
ATOM 16162 CD LYS D 1001 48.094 -15.740 -53.196 -0.002 1.700
ATOM 16163 HD2 LYS D 1001 47.247 -15.262 -52.703 0.064 1.200
ATOM 16164 HD3 LYS D 1001 47.813 -16.757 -53.471 0.065 1.200
ATOM 16165 CE LYS D 1001 49.220 -15.799 -52.239 0.001 1.700
ATOM 16166 HE2 LYS D 1001 48.845 -16.077 -51.254 0.065 1.200
ATOM 16167 HE3 LYS D 1001 49.700 -14.822 -52.182 0.064 1.200
ATOM 16168 NZ LYS D 1001 50.201 -16.804 -52.694 -0.140 1.550
ATOM 16169 HZ1 LYS D 1001 51.133 -16.497 -52.454 0.073 1.200
ATOM 16170 HZ2 LYS D 1001 50.011 -17.688 -52.244 0.072 1.200
ATOM 16171 HZ3 LYS D 1001 50.131 -16.914 -53.695 0.074 1.200
ATOM 16172 C LYS D 1001 46.869 -14.798 -57.141 0.028 1.700
ATOM 16173 O LYS D 1001 47.773 -15.266 -57.875 -0.253 1.520
The output is not in PDB format but in PQR, which, to my knowledge, has no exact definition. The exact format ChargeFW2 uses conforms to specifications, which are whitespace-delimited: https://docs.mdanalysis.org/1.0.0/documentation_pages/coordinates/PQR.html https://apbs.readthedocs.io/en/latest/formats/pqr.html
