[gmx-users] (no subject)
maya nair
mayasnair1 at gmail.com
Mon Dec 3 12:04:58 CET 2018
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
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