AMBER Archive (2004)

Subject: AMBER: Co-ordination error while running tleap

From: anita pachaimuthu (anita_pachaimuthu_at_lycos.com)
Date: Wed Jul 21 2004 - 10:12:12 CDT

Hi
Thanks Sebastien Osborne for helping me in the prev problem(loading the .lib file).

When i ran tleap this was the error message i got,can somebody help me understand the error

Error message:

Bond: Maximum coordination exceeded on .R<NDH 668>.A<H36 65>
      -- setting atoms pert=true overrides default limits
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 468
!FATAL: Message: debug
!
!ABORTING.
Abort (core dumped)

This is the input pdb file

ATOM 1 AC4 NDH 668 -1.883 14.087 2.149 1.00 0.00
ATOM 2 AN9 NDH 668 -2.035 13.040 2.987 1.00 0.00
ATOM 3 AC8 NDH 668 -3.356 12.798 3.114 1.00 0.00
ATOM 4 AN7 NDH 668 -4.045 13.610 2.352 1.00 0.00
ATOM 5 AC5 NDH 668 -3.125 14.486 1.826 1.00 0.00
ATOM 6 AC6 NDH 668 -3.285 15.677 1.045 1.00 0.00
ATOM 7 AN1 NDH 668 -2.208 16.207 0.480 1.00 0.00
ATOM 8 AC2 NDH 668 -0.979 15.789 0.880 1.00 0.00
ATOM 9 AN3 NDH 668 -0.718 14.735 1.714 1.00 0.00
ATOM 10 H20 NDH 668 -0.092 16.249 0.470 1.00 0.00
ATOM 11 AN6 NDH 668 -4.479 16.248 0.753 1.00 0.00
ATOM 12 H36 NDH 668 -4.382 16.123 0.059 1.00 0.00
ATOM 13 H21 NDH 668 -5.367 15.839 1.009 1.00 0.00
ATOM 14 H22 NDH 668 -3.754 12.018 3.746 1.00 0.00
ATOM 15 AC1* NDH 668 -0.918 12.396 3.724 1.00 0.00
ATOM 16 AO4* NDH 668 -0.439 11.398 2.956 1.00 0.00
ATOM 17 AC4* NDH 668 0.197 10.507 3.806 1.00 0.00
ATOM 18 AC3* NDH 668 -0.279 10.722 5.298 1.00 0.00
ATOM 19 AC2* NDH 668 -1.315 11.767 5.112 1.00 0.00
ATOM 20 H18 NDH 668 -2.260 11.249 4.949 1.00 0.00
ATOM 21 AO2* NDH 668 -1.469 12.761 6.161 1.00 0.00
ATOM 22 H23 NDH 668 -0.766 13.413 6.207 1.00 0.00
ATOM 23 H17 NDH 668 -0.677 9.822 5.768 1.00 0.00
ATOM 24 AO3* NDH 668 0.839 11.169 6.104 1.00 0.00
ATOM 25 H24 NDH 668 1.167 12.043 5.878 1.00 0.00
ATOM 26 AC5* NDH 668 0.060 9.075 3.292 1.00 0.00
ATOM 27 AO5* NDH 668 0.715 8.165 4.198 1.00 0.00
ATOM 28 AP NDH 668 -0.171 6.885 4.764 1.00 0.00
ATOM 29 O3 NDH 668 -0.443 6.127 3.399 1.00 0.00
ATOM 30 NP NDH 668 0.549 4.998 2.937 1.00 0.00
ATOM 31 NO5* NDH 668 0.039 4.766 1.474 1.00 0.00
ATOM 32 NC5* NDH 668 0.023 5.795 0.448 1.00 0.00
ATOM 33 NC4* NDH 668 -0.725 5.453 -0.868 1.00 0.00
ATOM 34 NC3* NDH 668 -2.125 4.824 -0.522 1.00 0.00
ATOM 35 NC2* NDH 668 -1.861 3.362 -0.629 1.00 0.00
ATOM 36 NC1* NDH 668 -1.024 3.421 -1.963 1.00 0.00
ATOM 37 NO4* NDH 668 -0.060 4.472 -1.681 1.00 0.00
ATOM 38 NN1 NDH 668 -0.249 2.266 -2.574 1.00 0.00
ATOM 39 NC6 NDH 668 0.547 1.772 -1.600 1.00 0.00
ATOM 40 NC5 NDH 668 0.243 0.795 -0.703 1.00 0.00
ATOM 41 NC4 NDH 668 -0.819 -0.091 -0.981 1.00 0.00
ATOM 42 NC3 NDH 668 -1.373 0.051 -2.408 1.00 0.00
ATOM 43 NC2 NDH 668 -1.007 1.264 -3.095 1.00 0.00
ATOM 44 H5 NDH 668 -1.881 1.463 -2.477 1.00 0.00
ATOM 45 NC7 NDH 668 -2.080 -1.027 -3.087 1.00 0.00
ATOM 46 NO7 NDH 668 -2.083 -2.158 -2.692 1.00 0.00
ATOM 47 NN7 NDH 668 -2.651 -0.807 -4.280 1.00 0.00
ATOM 48 H4 NDH 668 -3.040 -1.636 -4.707 1.00 0.00
ATOM 49 H72 NDH 668 -2.615 0.093 -4.735 1.00 0.00
ATOM 50 H3 NDH 668 -0.586 -1.149 -0.858 1.00 0.00
ATOM 51 H42 NDH 668 -1.626 0.229 -0.322 1.00 0.00
ATOM 52 H2 NDH 668 1.111 0.338 -0.229 1.00 0.00
ATOM 53 H1 NDH 668 1.510 1.447 -1.997 1.00 0.00
ATOM 54 H6 NDH 668 -1.622 3.829 -2.777 1.00 0.00
ATOM 55 H7 NDH 668 -1.200 2.910 0.110 1.00 0.00
ATOM 56 NO2* NDH 668 -2.986 2.515 -0.678 1.00 0.00
ATOM 57 H8 NDH 668 -2.888 1.891 0.045 1.00 0.00
ATOM 58 H9 NDH 668 -2.293 5.122 0.513 1.00 0.00
ATOM 59 NO3* NDH 668 -3.247 5.340 -1.272 1.00 0.00
ATOM 60 H10 NDH 668 -3.843 5.573 -0.556 1.00 0.00
ATOM 61 H11 NDH 668 -0.850 6.326 -1.508 1.00 0.00
ATOM 62 H12 NDH 668 -0.516 6.631 0.896 1.00 0.00
ATOM 63 H13 NDH 668 1.010 6.159 0.161 1.00 0.00
ATOM 64 NO2 NDH 668 1.950 5.576 2.903 1.00 0.00
ATOM 65 NO1 NDH 668 0.276 3.689 3.656 1.00 0.00
ATOM 66 AO1 NDH 668 -1.430 7.514 5.273 1.00 0.00
ATOM 67 AO2 NDH 668 0.578 6.016 5.711 1.00 0.00
ATOM 68 H15 NDH 668 0.506 9.015 2.299 1.00 0.00
ATOM 69 H14 NDH 668 -1.007 8.853 3.328 1.00 0.00
ATOM 70 H16 NDH 668 1.234 10.832 3.727 1.00 0.00
ATOM 71 H19 NDH 668 -0.186 13.200 3.810 1.00 0.00
TER 72 NDH 668
ATOM 73 N SER 1 27.127 18.424 -10.082 1.00 -0.26
ATOM 74 CA SER 1 26.095 19.014 -10.908 1.00 0.15
ATOM 75 C SER 1 25.267 19.933 -10.104 1.00 0.62
ATOM 76 O SER 1 25.477 20.031 -8.894 1.00 -0.50
ATOM 77 CB SER 1 25.181 17.970 -11.577 1.00 0.02
ATOM 78 OG SER 1

Thanks,
Anita 

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