ERROR 1 [file res.itp, line 57]: Invalid Atomnr j: 4, b2->nr: 3 I am getting the above error for the command
gmx grompp -f em.mdp -c solv.gro -p topol1.top -o ions.tpr. My res.itp file is given below. I couldnot understand the meaning of this error. Can you please help me? part of the .itp is appended here. 1. trial_GMX.top created by acpype (Rev: 0) on Wed Nov 21 15:15:35 2018 2. 3. 4. ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 5. 1 2 yes 0.5 0.8333 6. 7. # include "ffnonbonded.itp" 8. # include "ffbonded.itp" 9. # include "gbsa.itp" 10. 11. 12. ;name bond_type mass charge ptype sigma epsilon Amb 13. CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 14. oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 15. ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 16. ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 17. ce ce 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 18. cf cf 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 19. 20. 21. ;name nrexcl 22. STL 3 23. 24. ; nr type resi res atom cgnr charge mass ; qtot bond_type 25. 1 CA 1 STL C1 1 0.156600 12.01000 ; qtot 0.157 26. 2 oh 1 STL O1 2 -0.494100 16.00000 ; qtot -0.338 27. 3 ho 1 STL H1 3 0.420000 1.00800 ; qtot 0.083 28. 4 CA 1 STL C2 4 -0.185000 12.01000 ; qtot -0.103 29. 5 ha 1 STL H2 5 0.168000 1.00800 ; qtot 0.066 30. 6 oh 1 STL O2 6 -0.494100 16.00000 ; qtot -0.429 31. 7 ho 1 STL H5 7 0.420500 1.00800 ; qtot -0.008 32. 8 CA 1 STL C3 8 0.156600 12.01000 ; qtot 0.149 33. 9 oh 1 STL O3 9 -0.494100 16.00000 ; qtot -0.346 34. 10 ho 1 STL H3 10 0.420500 1.00800 ; qtot 0.075 35. 11 CA 1 STL C4 11 -0.240000 12.01000 ; qtot -0.165 36. 12 ha 1 STL H4 12 0.137000 1.00800 ; qtot -0.028 37. 13 CA 1 STL C5 13 0.023200 12.01000 ; qtot -0.005 38. 14 CA 1 STL C6 14 -0.240000 12.01000 ; qtot -0.245 39. 15 ha 1 STL H6 15 0.137000 1.00800 ; qtot -0.108 40. 16 ce 1 STL C7 16 -0.121200 12.01000 ; qtot -0.229 41. 17 ha 1 STL H7 17 0.130000 1.00800 ; qtot -0.099 42. 18 cf 1 STL C8 18 -0.085200 12.01000 ; qtot -0.184 43. 19 ha 1 STL H8 19 0.126000 1.00800 ; qtot -0.058 44. 20 CA 1 STL C9 20 -0.098800 12.01000 ; qtot -0.157 45. 21 CA 1 STL C10 21 -0.079500 12.01000 ; qtot -0.237 46. 22 ha 1 STL H10 22 0.136000 1.00800 ; qtot -0.101 47. 23 CA 1 STL C11 23 -0.187000 12.01000 ; qtot -0.288 48. 24 ha 1 STL H11 24 0.143500 1.00800 ; qtot -0.144 49. 25 CA 1 STL C12 25 0.131100 12.01000 ; qtot -0.013 50. 26 CA 1 STL C13 26 -0.187000 12.01000 ; qtot -0.200 51. 27 ha 1 STL H13 27 0.143500 1.00800 ; qtot -0.057 52. 28 CA 1 STL C14 28 -0.079500 12.01000 ; qtot -0.136 53. 29 ha 1 STL H14 29 0.136000 1.00800 ; qtot 0.000 54. 55. 56. ; ai aj funct r k 57. 1 4 1 1.3984e-01 3.8585e+05 ; C1 - C2 58. 1 9 1 1.3637e-01 3.2133e+05 ; C1 - O3 59. 1 14 1 1.3984e-01 3.8585e+05 ; C1 - C6 60. 2 3 1 9.7300e-02 3.1079e+05 ; O1 - H1 61. 2 25 1 1.3637e-01 3.2133e+05 ; O1 - C12 62. 4 5 1 1.0860e-01 2.8937e+05 ; C2 - H2 63. 4 8 1 1.3984e-01 3.8585e+05 ; C2 - C3 64. 6 7 1 9.7300e-02 3.1079e+05 ; O2 - H5 65. 6 8 1 1.3637e-01 3.2133e+05 ; O2 - C3 66. 8 11 1 1.3984e-01 3.8585e+05 ; C3 - C4 67. 9 10 1 9.7300e-02 3.1079e+05 ; O3 - H3 68. 11 12 1 1.0860e-01 2.8937e+05 ; C4 - H4 69. 11 13 1 1.3984e-01 3.8585e+05 ; C4 - C5 70. 13 14 1 1.3984e-01 3.8585e+05 ; C5 - C6 71. 13 16 1 1.4763e-01 3.0234e+05 ; C5 - C7 72. 14 15 1 1.0860e-01 2.8937e+05 ; C6 - H6 73. 16 17 1 1.0883e-01 2.8660e+05 ; C7 - H7 74. 16 18 1 1.3509e-01 4.5070e+05 ; C7 - C8 75. 18 19 1 1.0883e-01 2.8660e+05 ; C8 - H8 76. 18 20 1 1.4763e-01 3.0234e+05 ; C8 - C9 77. 20 21 1 1.3984e-01 3.8585e+05 ; C9 - C10 78. 20 28 1 1.3984e-01 3.8585e+05 ; C9 - C14 79. 21 22 1 1.0860e-01 2.8937e+05 ; C10 - H10 80. 21 23 1 1.3984e-01 3.8585e+05 ; C10 - C11 81. 23 24 1 1.0860e-01 2.8937e+05 ; C11 - H11 82. 23 25 1 1.3984e-01 3.8585e+05 ; C11 - C12 83. 25 26 1 1.3984e-01 3.8585e+05 ; C12 - C13 84. 26 27 1 1.0860e-01 2.8937e+05 ; C13 - H13 85. 26 28 1 1.3984e-01 3.8585e+05 ; C13 - C14 86. 28 29 1 1.0860e-01 2.8937e+05 ; C14 - H14 -- Maya S Nair Assistant Professor Department of Biotechnology IIT Roorkee India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
