[gmx-users] (no subject)

[maya nair]

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