[gmx-users] CHARMM-GUI files give error in Gromacs
gozde ergin
gozdeeergin at gmail.com
Fri Sep 2 16:28:28 CEST 2016
Dear all,
I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid.
After that I used genbox command of gromacs and add some water molecules.
When I try to run I get 100 Errors saying :
No default bond types, No default U-B types, No default Proper Dih. types, No default Improper Dih. types.
All these errors are related to .itp file. However .itp files seems correct:
Any help would be appreciated. Thanks.
;;
;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
;;
;; psf2itp_mol.py
;;
;; Correspondance:
;; j712l362 at ku.edu or wonpil at ku.edu
;;
;; GROMACS topology file for LIG
;;
[ moleculetype ]
; name nrexcl
LIG 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG3C41 1 LIG C2 1 -0.087 12.0110 ; qtot -0.087
2 CG3C41 1 LIG C1 2 -0.046 12.0110 ; qtot -0.133
3 HGA1 1 LIG H1 3 0.090 1.0080 ; qtot -0.043
4 CG3C41 1 LIG C3 4 -0.038 12.0110 ; qtot -0.081
5 CG2O5 1 LIG C8 5 0.388 12.0110 ; qtot 0.307
6 HGA1 1 LIG H2 6 0.090 1.0080 ; qtot 0.397
7 OG2D3 1 LIG O1 7 -0.481 15.9994 ; qtot -0.084
8 CG331 1 LIG C10 8 -0.229 12.0110 ; qtot -0.313
9 HGA3 1 LIG H14 9 0.090 1.0080 ; qtot -0.223
10 HGA3 1 LIG H15 10 0.090 1.0080 ; qtot -0.133
11 HGA3 1 LIG H13 11 0.090 1.0080 ; qtot -0.043
12 CG3C41 1 LIG C4 12 -0.178 12.0110 ; qtot -0.221
13 HGA2 1 LIG H4 13 0.090 1.0080 ; qtot -0.131
14 HGA2 1 LIG H3 14 0.090 1.0080 ; qtot -0.041
15 CG331 1 LIG C6 15 -0.248 12.0110 ; qtot -0.289
16 HGA3 1 LIG H10 16 0.090 1.0080 ; qtot -0.199
17 HGA3 1 LIG H9 17 0.090 1.0080 ; qtot -0.109
18 HGA3 1 LIG H8 18 0.090 1.0080 ; qtot -0.019
19 CG331 1 LIG C5 19 -0.248 12.0110 ; qtot -0.267
20 HGA3 1 LIG H6 20 0.090 1.0080 ; qtot -0.177
21 HGA3 1 LIG H7 21 0.090 1.0080 ; qtot -0.087
22 HGA3 1 LIG H5 22 0.090 1.0080 ; qtot 0.003
23 CG321 1 LIG C7 23 -0.207 12.0110 ; qtot -0.204
24 CG2O2 1 LIG C9 24 0.803 12.0110 ; qtot 0.599
25 HGA2 1 LIG H12 25 0.090 1.0080 ; qtot 0.689
26 HGA2 1 LIG H11 26 0.090 1.0080 ; qtot 0.779
27 OG2D1 1 LIG O3 27 -0.576 15.9994 ; qtot 0.203
28 OG311 1 LIG O2 28 -0.632 15.9994 ; qtot -0.429
29 HGP1 1 LIG H16 29 0.429 1.0080 ; qtot 0.000
[ bonds ]
; ai aj funct b0 Kb
1 2 1
1 3 1
1 12 1
1 23 1
2 4 1
2 15 1
2 19 1
4 5 1
4 6 1
4 12 1
5 7 1
5 8 1
8 9 1
8 10 1
8 11 1
12 13 1
12 14 1
15 16 1
15 17 1
15 18 1
19 20 1
19 21 1
19 22 1
23 24 1
23 25 1
23 26 1
24 27 1
24 28 1
28 29 1
[ pairs ]
; ai aj funct c6 c12
1 2 1
1 5 1
1 6 1
1 12 1
1 16 1
1 17 1
1 18 1
1 20 1
1 21 1
1 22 1
1 27 1
1 28 1
2 4 1
2 7 1
2 8 1
2 13 1
2 14 1
2 24 1
2 25 1
2 26 1
3 4 1
3 13 1
3 14 1
3 15 1
3 19 1
3 24 1
3 25 1
3 26 1
4 9 1
4 10 1
4 11 1
4 12 1
4 16 1
4 17 1
4 18 1
4 20 1
4 21 1
4 22 1
4 23 1
5 13 1
5 14 1
5 15 1
5 19 1
6 7 1
6 8 1
6 13 1
6 14 1
6 15 1
6 19 1
7 9 1
7 10 1
7 11 1
7 12 1
8 12 1
12 15 1
12 19 1
12 24 1
12 25 1
12 26 1
13 23 1
14 23 1
15 20 1
15 21 1
15 22 1
15 23 1
16 19 1
17 19 1
18 19 1
19 23 1
23 29 1
25 27 1
25 28 1
26 27 1
26 28 1
27 29 1
[ angles ]
; ai aj ak funct th0 cth S0 Kub
2 1 3 5
2 1 12 5
2 1 23 5
3 1 12 5
3 1 23 5
12 1 23 5
1 2 4 5
1 2 15 5
1 2 19 5
4 2 15 5
4 2 19 5
15 2 19 5
2 4 5 5
2 4 6 5
2 4 12 5
5 4 6 5
5 4 12 5
6 4 12 5
4 5 7 5
4 5 8 5
7 5 8 5
5 8 9 5
5 8 10 5
5 8 11 5
9 8 10 5
9 8 11 5
10 8 11 5
1 12 4 5
1 12 13 5
1 12 14 5
4 12 13 5
4 12 14 5
13 12 14 5
2 15 16 5
2 15 17 5
2 15 18 5
16 15 17 5
16 15 18 5
17 15 18 5
2 19 20 5
2 19 21 5
2 19 22 5
20 19 21 5
20 19 22 5
21 19 22 5
1 23 24 5
1 23 25 5
1 23 26 5
24 23 25 5
24 23 26 5
25 23 26 5
23 24 27 5
23 24 28 5
27 24 28 5
24 28 29 5
[ dihedrals ]
; ai aj ak al funct phi0 cp mult
3 1 2 4 9
3 1 2 15 9
3 1 2 19 9
12 1 2 15 9
12 1 2 19 9
2 1 12 4 9
2 1 12 13 9
2 1 12 14 9
3 1 12 4 9
3 1 12 13 9
3 1 12 14 9
2 1 23 24 9
2 1 23 25 9
2 1 23 26 9
3 1 23 24 9
3 1 23 25 9
3 1 23 26 9
12 1 23 24 9
12 1 23 25 9
12 1 23 26 9
4 2 1 12 9
4 2 1 23 9
15 2 1 23 9
19 2 1 23 9
1 2 4 5 9
1 2 4 6 9
1 2 4 12 9
1 2 15 16 9
1 2 15 17 9
1 2 15 18 9
4 2 15 16 9
4 2 15 17 9
4 2 15 18 9
1 2 19 20 9
1 2 19 21 9
1 2 19 22 9
4 2 19 20 9
4 2 19 21 9
4 2 19 22 9
15 2 19 20 9
15 2 19 21 9
15 2 19 22 9
5 4 2 15 9
5 4 2 19 9
6 4 2 15 9
6 4 2 19 9
12 4 2 15 9
12 4 2 19 9
2 4 5 7 9
2 4 5 8 9
6 4 5 7 9
6 4 5 8 9
2 4 12 13 9
2 4 12 14 9
5 4 12 13 9
5 4 12 14 9
6 4 12 13 9
6 4 12 14 9
7 5 4 12 9
8 5 4 12 9
4 5 8 9 9
4 5 8 10 9
4 5 8 11 9
7 5 8 9 9
7 5 8 10 9
7 5 8 11 9
4 12 1 23 9
13 12 1 23 9
14 12 1 23 9
1 12 4 2 9
1 12 4 5 9
1 12 4 6 9
16 15 2 19 9
17 15 2 19 9
18 15 2 19 9
1 23 24 27 9
1 23 24 28 9
25 23 24 27 9
25 23 24 28 9
26 23 24 27 9
26 23 24 28 9
23 24 28 29 9
27 24 28 29 9
[ dihedrals ]
; ai aj ak al funct q0 cq
5 8 4 7 2
24 23 27 28 2
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