# Grompp Fatal error: Invalid bond type **URL:** \ **Category:** User discussions\ **Created:** [October 15, 2020, 5:08am UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960 "2020-10-15T05:08:47Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![swamybioinfo](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@swamybioinfo](https://gromacs.bioexcel.eu/u/swamybioinfo)\ **Post date:** [October 15, 2020, 5:08am UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960/1 "2020-10-15T05:08:47Z")
GROMACS version:version 2020.3 GROMACS modification: Yes/No Dear Sir, I am unable find the solution for following error gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Fatal error: Invalid bond type 0 The following file is lig1.itp file. ; Created by cgenff\_charmm2gmx.py [moleculetype] ; Name nrexcl LIG1 3 [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 LIG1 rtp LIG1 q qsum 1 CG3C51 1 LIG1 C1 1 0.084 12.011 ; 2 NG3C51 1 LIG1 N1 2 -0.479 14.007 ; 3 OG311 1 LIG1 O1 3 -0.652 15.999 ; 4 CG311 1 LIG1 C2 4 -0.055 12.011 ; 5 NG311 1 LIG1 N2 5 -0.727 14.007 ; 6 OG311 1 LIG1 O2 6 -0.649 15.999 ; 7 CG3C52 1 LIG1 C3 7 0.093 12.011 ; 8 OG311 1 LIG1 O3 8 -0.617 15.999 ; 9 CG3C52 1 LIG1 C4 9 -0.212 12.011 ; 10 OG311 1 LIG1 O4 10 -0.617 15.999 ; 11 CG3C52 1 LIG1 C5 11 -0.214 12.011 ; 12 CG321 1 LIG1 C6 12 -0.168 12.011 ; 13 CG321 1 LIG1 C7 13 -0.168 12.011 ; 14 CG321 1 LIG1 C8 14 0.122 12.011 ; 15 CG321 1 LIG1 C9 15 -0.178 12.011 ; 16 CG321 1 LIG1 C10 16 -0.178 12.011 ; 17 CG311 1 LIG1 C11 17 0.006 12.011 ; 18 CG311 1 LIG1 C12 18 0.137 12.011 ; 19 CG321 1 LIG1 C13 19 -0.163 12.011 ; 20 CG311 1 LIG1 C14 20 -0.096 12.011 ; 21 CG321 1 LIG1 C15 21 -0.169 12.011 ; 22 CG311 1 LIG1 C16 22 0.138 12.011 ; 23 CG321 1 LIG1 C17 23 -0.179 12.011 ; 24 CG311 1 LIG1 C18 24 0.408 12.011 ; 25 HGA1 1 LIG1 H01 25 0.090 1.008 ; 26 HGA1 1 LIG1 H02 26 0.090 1.008 ; 27 HGPAM1 1 LIG1 H03 27 0.347 1.008 ; 28 HGA2 1 LIG1 H04 28 0.090 1.008 ; 29 HGP1 1 LIG1 H05 29 0.369 1.008 ; 30 HGA2 1 LIG1 H06 30 0.090 1.008 ; 31 HGP1 1 LIG1 H07 31 0.369 1.008 ; 32 HGA2 1 LIG1 H08 32 0.090 1.008 ; 33 HGA2 1 LIG1 H09 33 0.090 1.008 ; 34 HGA2 1 LIG1 H14 34 0.090 1.008 ; 35 HGA2 1 LIG1 H15 35 0.090 1.008 ; 36 HGA2 1 LIG1 H16 36 0.090 1.008 ; 37 HGA2 1 LIG1 H17 37 0.090 1.008 ; 38 HGA1 1 LIG1 H18 38 0.090 1.008 ; 39 HGA1 1 LIG1 H19 39 0.090 1.008 ; 40 HGA2 1 LIG1 H20 40 0.090 1.008 ; 41 HGA1 1 LIG1 H21 41 0.090 1.008 ; 42 HGA2 1 LIG1 H22 42 0.090 1.008 ; 43 HGA1 1 LIG1 H23 43 0.090 1.008 ; 44 HGA2 1 LIG1 H24 44 0.090 1.008 ; 45 HGA1 1 LIG1 H25 45 0.090 1.008 ; 46 HGA2 1 LIG1 H1 46 0.090 1.008 ; 47 HGA2 1 LIG1 H2 47 0.090 1.008 ; 48 HGA2 1 LIG1 H3 48 0.090 1.008 ; 49 HGA2 1 LIG1 H4 49 0.090 1.008 ; 50 HGA2 1 LIG1 H5 50 0.090 1.008 ; 51 HGA2 1 LIG1 H6 51 0.090 1.008 ; 52 HGA2 1 LIG1 H7 52 0.090 1.008 ; 53 HGA2 1 LIG1 H8 53 0.090 1.008 ; 54 HGA2 1 LIG1 H9 54 0.090 1.008 ; 55 HGA2 1 LIG1 H10 55 0.090 1.008 ; 56 HGA2 1 LIG1 H11 56 0.090 1.008 ; 57 HGP1 1 LIG1 H12 57 0.419 1.008 ; 58 HGP1 1 LIG1 H13 58 0.419 1.008 ; [bonds] ; ai aj funct c0 c1 c2 c3 1 2 1 ; CG3C51 NG3C51 1 9 1 ; CG3C51 CG3C52 1 14 1 ; CG3C51 CG321 1 25 1 ; CG3C51 HGA1 2 4 1 ; NG3C51 CG311 2 7 1 ; NG3C51 CG3C52 3 57 1 ; OG311 HGP1 3 18 1 ; OG311 CG311 4 12 1 ; CG311 CG321 4 13 1 ; CG311 CG321 4 26 1 ; CG311 HGA1 5 14 1 ; NG311 CG321 5 27 1 ; NG311 HGPAM1 5 17 1 ; NG311 CG311 6 58 1 ; OG311 HGP1 6 22 1 ; OG311 CG311 7 11 1 ; CG3C52 CG3C52 7 28 1 ; CG3C52 HGA2 7 46 1 ; CG3C52 HGA2 8 24 1 ; OG311 CG311 8 29 1 ; OG311 HGP1 9 11 1 ; CG3C52 CG3C52 9 30 1 ; CG3C52 HGA2 9 47 1 ; CG3C52 HGA2 10 24 1 ; OG311 CG311 10 31 1 ; OG311 HGP1 11 32 1 ; CG3C52 HGA2 11 48 1 ; CG3C52 HGA2 12 15 1 ; CG321 CG321 12 33 1 ; CG321 HGA2 12 49 1 ; CG321 HGA2 13 16 1 ; CG321 CG321 13 34 1 ; CG321 HGA2 13 50 1 ; CG321 HGA2 14 35 1 ; CG321 HGA2 14 51 1 ; CG321 HGA2 15 18 1 ; CG321 CG311 15 36 1 ; CG321 HGA2 15 52 1 ; CG321 HGA2 16 18 1 ; CG321 CG311 16 37 1 ; CG321 HGA2 16 53 1 ; CG321 HGA2 17 19 1 ; CG311 CG321 17 21 1 ; CG311 CG321 17 38 1 ; CG311 HGA1 18 39 1 ; CG311 HGA1 19 20 1 ; CG321 CG311 19 40 1 ; CG321 HGA2 19 54 1 ; CG321 HGA2 20 22 1 ; CG311 CG311 20 24 1 ; CG311 CG311 20 41 1 ; CG311 HGA1 21 23 1 ; CG321 CG321 21 42 1 ; CG321 HGA2 21 55 1 ; CG321 HGA2 22 23 1 ; CG311 CG321 22 43 1 ; CG311 HGA1 23 44 1 ; CG321 HGA2 23 56 1 ; CG321 HGA2 24 45 1 ; CG311 HGA1 [pairs] ; ai aj funct c0 c1 c2 c3 1 12 1 1 13 1 1 26 1 1 28 1 1 46 1 1 27 1 1 17 1 1 32 1 1 48 1 2 30 1 2 47 1 2 5 1 2 35 1 2 51 1 2 15 1 2 33 1 2 49 1 2 16 1 2 34 1 2 50 1 2 32 1 2 48 1 3 12 1 3 36 1 3 52 1 3 13 1 3 37 1 3 53 1 4 9 1 4 14 1 4 25 1 4 11 1 4 28 1 4 46 1 4 18 1 4 36 1 4 52 1 4 37 1 4 53 1 5 9 1 5 25 1 5 20 1 5 40 1 5 54 1 5 23 1 5 42 1 5 55 1 6 19 1 6 24 1 6 41 1 6 21 1 6 44 1 6 56 1 7 14 1 7 25 1 7 12 1 7 13 1 7 26 1 7 30 1 7 47 1 8 31 1 8 19 1 8 22 1 8 41 1 9 35 1 9 51 1 9 28 1 9 46 1 10 29 1 10 19 1 10 22 1 10 41 1 11 14 1 11 25 1 12 16 1 12 34 1 12 50 1 12 39 1 13 15 1 13 33 1 13 49 1 13 39 1 14 30 1 14 47 1 14 19 1 14 21 1 14 38 1 15 57 1 15 26 1 15 37 1 15 53 1 16 57 1 16 26 1 16 36 1 16 52 1 17 35 1 17 51 1 17 22 1 17 24 1 17 41 1 17 44 1 17 56 1 18 33 1 18 49 1 18 34 1 18 50 1 19 27 1 19 23 1 19 42 1 19 55 1 19 43 1 19 45 1 20 58 1 20 29 1 20 31 1 20 21 1 20 38 1 20 44 1 20 56 1 21 27 1 21 40 1 21 54 1 21 43 1 22 40 1 22 54 1 22 45 1 22 42 1 22 55 1 23 58 1 23 38 1 23 24 1 23 41 1 24 40 1 24 54 1 24 43 1 25 30 1 25 47 1 25 35 1 25 51 1 26 33 1 26 49 1 26 34 1 26 50 1 27 35 1 27 51 1 27 38 1 28 32 1 28 48 1 29 45 1 30 32 1 30 48 1 10 24 20 5 ; OG311 CG311 CG311 10 24 45 5 ; OG311 CG311 HGA1 20 24 45 5 ; CG311 CG311 HGA1 [dihedrals] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 9 1 2 4 9 ; CG3C52 CG3C51 NG3C51 CG311 9 1 2 7 9 ; CG3C52 CG3C51 NG3C51 CG3C52 14 1 2 4 9 ; CG321 CG3C51 NG3C51 CG311 14 1 2 7 9 ; CG321 CG3C51 NG3C51 CG3C52 25 1 2 4 9 ; HGA1 CG3C51 NG3C51 CG311 25 1 2 7 9 ; HGA1 CG3C51 NG3C51 CG3C52 2 1 9 11 9 ; NG3C51 CG3C51 CG3C52 CG3C52 2 1 9 30 9 ; NG3C51 CG3C51 CG3C52 HGA2 2 1 9 47 9 ; NG3C51 CG3C51 CG3C52 HGA2 14 1 9 11 9 ; CG321 CG3C51 CG3C52 CG3C52 14 1 9 30 9 ; CG321 CG3C51 CG3C52 HGA2 14 1 9 47 9 ; CG321 CG3C51 CG3C52 HGA2 25 1 9 11 9 ; HGA1 CG3C51 CG3C52 CG3C52 25 1 9 30 9 ; HGA1 CG3C51 CG3C52 HGA2 25 1 9 47 9 ; HGA1 CG3C51 CG3C52 HGA2 2 1 14 5 9 ; NG3C51 CG3C51 CG321 NG311 2 1 14 35 9 ; NG3C51 CG3C51 CG321 HGA2 2 1 14 51 9 ; NG3C51 CG3C51 CG321 HGA2 9 1 14 5 9 ; CG3C52 CG3C51 CG321 NG311 9 1 14 35 9 ; CG3C52 CG3C51 CG321 HGA2 9 1 14 51 9 ; CG3C52 CG3C51 CG321 HGA2 25 1 14 5 9 ; HGA1 CG3C51 CG321 NG311 25 1 14 35 9 ; HGA1 CG3C51 CG321 HGA2 25 1 14 51 9 ; HGA1 CG3C51 CG321 HGA2 1 2 4 12 9 ; CG3C51 NG3C51 CG311 CG321 1 2 4 13 9 ; CG3C51 NG3C51 CG311 CG321 1 2 4 26 9 ; CG3C51 NG3C51 CG311 HGA1 7 2 4 12 9 ; CG3C52 NG3C51 CG311 CG321 7 2 4 13 9 ; CG3C52 NG3C51 CG311 CG321 7 2 4 26 9 ; CG3C52 NG3C51 CG311 HGA1 1 2 7 11 9 ; CG3C51 NG3C51 CG3C52 CG3C52 1 2 7 28 9 ; CG3C51 NG3C51 CG3C52 HGA2 1 2 7 46 9 ; CG3C51 NG3C51 CG3C52 HGA2 4 2 7 11 9 ; CG311 NG3C51 CG3C52 CG3C52 4 2 7 28 9 ; CG311 NG3C51 CG3C52 HGA2 4 2 7 46 9 ; CG311 NG3C51 CG3C52 HGA2 57 3 18 15 9 ; HGP1 OG311 CG311 CG321 57 3 18 16 9 ; HGP1 OG311 CG311 CG321 57 3 18 39 9 ; HGP1 OG311 CG311 HGA1 2 4 12 15 9 ; NG3C51 CG311 CG321 CG321 2 4 12 33 9 ; NG3C51 CG311 CG321 HGA2 2 4 12 49 9 ; NG3C51 CG311 CG321 HGA2 13 4 12 15 9 ; CG321 CG311 CG321 CG321 13 4 12 33 9 ; CG321 CG311 CG321 HGA2 13 4 12 49 9 ; CG321 CG311 CG321 HGA2 26 4 12 15 9 ; HGA1 CG311 CG321 CG321 26 4 12 33 9 ; HGA1 CG311 CG321 HGA2 26 4 12 49 9 ; HGA1 CG311 CG321 HGA2 2 4 13 16 9 ; NG3C51 CG311 CG321 CG321 2 4 13 34 9 ; NG3C51 CG311 CG321 HGA2 2 4 13 50 9 ; NG3C51 CG311 CG321 HGA2 12 4 13 16 9 ; CG321 CG311 CG321 CG321 12 4 13 34 9 ; CG321 CG311 CG321 HGA2 12 4 13 50 9 ; CG321 CG311 CG321 HGA2 26 4 13 16 9 ; HGA1 CG311 CG321 CG321 26 4 13 34 9 ; HGA1 CG311 CG321 HGA2 26 4 13 50 9 ; HGA1 CG311 CG321 HGA2 27 5 14 1 9 ; HGPAM1 NG311 CG321 CG3C51 27 5 14 35 9 ; HGPAM1 NG311 CG321 HGA2 27 5 14 51 9 ; HGPAM1 NG311 CG321 HGA2 17 5 14 1 9 ; CG311 NG311 CG321 CG3C51 17 5 14 35 9 ; CG311 NG311 CG321 HGA2 17 5 14 51 9 ; CG311 NG311 CG321 HGA2 14 5 17 19 9 ; CG321 NG311 CG311 CG321 14 5 17 21 9 ; CG321 NG311 CG311 CG321 14 5 17 38 9 ; CG321 NG311 CG311 HGA1 27 5 17 19 9 ; HGPAM1 NG311 CG311 CG321 27 5 17 21 9 ; HGPAM1 NG311 CG311 CG321 27 5 17 38 9 ; HGPAM1 NG311 CG311 HGA1 58 6 22 20 9 ; HGP1 OG311 CG311 CG311 58 6 22 23 9 ; HGP1 OG311 CG311 CG321 58 6 22 43 9 ; HGP1 OG311 CG311 HGA1 2 7 11 9 9 ; NG3C51 CG3C52 CG3C52 CG3C52 2 7 11 32 9 ; NG3C51 CG3C52 CG3C52 HGA2 2 7 11 48 9 ; NG3C51 CG3C52 CG3C52 HGA2 28 7 11 9 9 ; HGA2 CG3C52 CG3C52 CG3C52 28 7 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2 28 7 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2 46 7 11 9 9 ; HGA2 CG3C52 CG3C52 CG3C52 46 7 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2 46 7 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2 29 8 24 10 9 ; HGP1 OG311 CG311 OG311 29 8 24 20 9 ; HGP1 OG311 CG311 CG311 29 8 24 45 9 ; HGP1 OG311 CG311 HGA1 1 9 11 7 9 ; CG3C51 CG3C52 CG3C52 CG3C52 1 9 11 32 9 ; CG3C51 CG3C52 CG3C52 HGA2 1 9 11 48 9 ; CG3C51 CG3C52 CG3C52 HGA2 30 9 11 7 9 ; HGA2 CG3C52 CG3C52 CG3C52 30 9 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2 30 9 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2 47 9 11 7 9 ; HGA2 CG3C52 CG3C52 CG3C52 47 9 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2 47 9 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2 31 10 24 8 9 ; HGP1 OG311 CG311 OG311 31 10 24 20 9 ; HGP1 OG311 CG311 CG311 31 10 24 45 9 ; HGP1 OG311 CG311 HGA1 4 12 15 18 9 ; CG311 CG321 CG321 CG311 4 12 15 36 9 ; CG311 CG321 CG321 HGA2 4 12 15 52 9 ; CG311 CG321 CG321 HGA2 33 12 15 18 9 ; HGA2 CG321 CG321 CG311 33 12 15 36 9 ; HGA2 CG321 CG321 HGA2 33 12 15 52 9 ; HGA2 CG321 CG321 HGA2 49 12 15 18 9 ; HGA2 CG321 CG321 CG311 49 12 15 36 9 ; HGA2 CG321 CG321 HGA2 49 12 15 52 9 ; HGA2 CG321 CG321 HGA2 4 13 16 18 9 ; CG311 CG321 CG321 CG311 4 13 16 37 9 ; CG311 CG321 CG321 HGA2 4 13 16 53 9 ; CG311 CG321 CG321 HGA2 34 13 16 18 9 ; HGA2 CG321 CG321 CG311 34 13 16 37 9 ; HGA2 CG321 CG321 HGA2 34 13 16 53 9 ; HGA2 CG321 CG321 HGA2 50 13 16 18 9 ; HGA2 CG321 CG321 CG311 50 13 16 37 9 ; HGA2 CG321 CG321 HGA2 50 13 16 53 9 ; HGA2 CG321 CG321 HGA2 12 15 18 3 9 ; CG321 CG321 CG311 OG311 12 15 18 16 9 ; CG321 CG321 CG311 CG321 12 15 18 39 9 ; CG321 CG321 CG311 HGA1 36 15 18 3 9 ; HGA2 CG321 CG311 OG311 36 15 18 16 9 ; HGA2 CG321 CG311 CG321 36 15 18 39 9 ; HGA2 CG321 CG311 HGA1 52 15 18 3 9 ; HGA2 CG321 CG311 OG311 52 15 18 16 9 ; HGA2 CG321 CG311 CG321 52 15 18 39 9 ; HGA2 CG321 CG311 HGA1 13 16 18 3 9 ; CG321 CG321 CG311 OG311 13 16 18 15 9 ; CG321 CG321 CG311 CG321 13 16 18 39 9 ; CG321 CG321 CG311 HGA1 37 16 18 3 9 ; HGA2 CG321 CG311 OG311 37 16 18 15 9 ; HGA2 CG321 CG311 CG321 37 16 18 39 9 ; HGA2 CG321 CG311 HGA1 53 16 18 3 9 ; HGA2 CG321 CG311 OG311 53 16 18 15 9 ; HGA2 CG321 CG311 CG321 53 16 18 39 9 ; HGA2 CG321 CG311 HGA1 5 17 19 20 9 ; NG311 CG311 CG321 CG311 5 17 19 40 9 ; NG311 CG311 CG321 HGA2 5 17 19 54 9 ; NG311 CG311 CG321 HGA2 21 17 19 20 9 ; CG321 CG311 CG321 CG311 21 17 19 40 9 ; CG321 CG311 CG321 HGA2 21 17 19 54 9 ; CG321 CG311 CG321 HGA2 38 17 19 20 9 ; HGA1 CG311 CG321 CG311 38 17 19 40 9 ; HGA1 CG311 CG321 HGA2 38 17 19 54 9 ; HGA1 CG311 CG321 HGA2 5 17 21 23 9 ; NG311 CG311 CG321 CG321 5 17 21 42 9 ; NG311 CG311 CG321 HGA2 5 17 21 55 9 ; NG311 CG311 CG321 HGA2 19 17 21 23 9 ; CG321 CG311 CG321 CG321 19 17 21 42 9 ; CG321 CG311 CG321 HGA2 19 17 21 55 9 ; CG321 CG311 CG321 HGA2 38 17 21 23 9 ; HGA1 CG311 CG321 CG321 38 17 21 42 9 ; HGA1 CG311 CG321 HGA2 38 17 21 55 9 ; HGA1 CG311 CG321 HGA2 17 19 20 22 9 ; CG311 CG321 CG311 CG311 17 19 20 24 9 ; CG311 CG321 CG311 CG311 17 19 20 41 9 ; CG311 CG321 CG311 HGA1 40 19 20 22 9 ; HGA2 CG321 CG311 CG311 40 19 20 24 9 ; HGA2 CG321 CG311 CG311 40 19 20 41 9 ; HGA2 CG321 CG311 HGA1 54 19 20 22 9 ; HGA2 CG321 CG311 CG311 54 19 20 24 9 ; HGA2 CG321 CG311 CG311 54 19 20 41 9 ; HGA2 CG321 CG311 HGA1 19 20 22 6 9 ; CG321 CG311 CG311 OG311 19 20 22 23 9 ; CG321 CG311 CG311 CG321 19 20 22 43 9 ; CG321 CG311 CG311 HGA1 24 20 22 6 9 ; CG311 CG311 CG311 OG311 24 20 22 23 9 ; CG311 CG311 CG311 CG321 24 20 22 43 9 ; CG311 CG311 CG311 HGA1 41 20 22 6 9 ; HGA1 CG311 CG311 OG311 41 20 22 23 9 ; HGA1 CG311 CG311 CG321 41 20 22 43 9 ; HGA1 CG311 CG311 HGA1 19 20 24 8 9 ; CG321 CG311 CG311 OG311 19 20 24 10 9 ; CG321 CG311 CG311 OG311 19 20 24 45 9 ; CG321 CG311 CG311 HGA1 22 20 24 8 9 ; CG311 CG311 CG311 OG311 22 20 24 10 9 ; CG311 CG311 CG311 OG311 22 20 24 45 9 ; CG311 CG311 CG311 HGA1 41 20 24 8 9 ; HGA1 CG311 CG311 OG311 41 20 24 10 9 ; HGA1 CG311 CG311 OG311 41 20 24 45 9 ; HGA1 CG311 CG311 HGA1 17 21 23 22 9 ; CG311 CG321 CG321 CG311 17 21 23 44 9 ; CG311 CG321 CG321 HGA2 17 21 23 56 9 ; CG311 CG321 CG321 HGA2 42 21 23 22 9 ; HGA2 CG321 CG321 CG311 42 21 23 44 9 ; HGA2 CG321 CG321 HGA2 42 21 23 56 9 ; HGA2 CG321 CG321 HGA2 55 21 23 22 9 ; HGA2 CG321 CG321 CG311 55 21 23 44 9 ; HGA2 CG321 CG321 HGA2 55 21 23 56 9 ; HGA2 CG321 CG321 HGA2 6 22 23 21 9 ; OG311 CG311 CG321 CG321 6 22 23 44 9 ; OG311 CG311 CG321 HGA2 6 22 23 56 9 ; OG311 CG311 CG321 HGA2 20 22 23 21 9 ; CG311 CG311 CG321 CG321 20 22 23 44 9 ; CG311 CG311 CG321 HGA2 20 22 23 56 9 ; CG311 CG311 CG321 HGA2 43 22 23 21 9 ; HGA1 CG311 CG321 CG321 43 22 23 44 9 ; HGA1 CG311 CG321 HGA2 43 22 23 56 9 ; HGA1 CG311 CG321 HGA2 lig1.gro Gallium Rubidium Oxygen Manganese Argon Carbon Silicon 58 1LIG1 C1 1 21.421 18.273 25.981 1LIG1 N1 2 21.391 18.209 26.101 1LIG1 O1 3 21.293 17.669 26.167 1LIG1 C2 4 21.361 18.073 26.124 1LIG1 N2 5 21.371 18.099 25.821 1LIG1 O2 6 21.348 17.844 25.327 1LIG1 C3 7 21.402 18.302 26.203 1LIG1 O3 8 21.699 18.056 25.433 1LIG1 C4 9 21.451 18.405 26.013 1LIG1 O4 10 21.589 17.963 25.266 . . . . ``` 1LIG1 C17 23 21.253 17.909 25.530 1LIG1 C18 24 21.596 18.003 25.385 1LIG1 H01 25 21.411 18.234 25.880 1LIG1 H02 26 21.276 18.057 26.191 1LIG1 H03 27 21.418 18.030 25.879 1LIG1 H04 28 21.398 18.339 26.305 1LIG1 H05 29 21.730 18.004 25.507 1LIG1 H06 30 21.479 18.480 25.939 1LIG1 H07 31 21.530 17.888 25.261 1LIG1 H08 32 21.447 18.518 26.204 1LIG1 H09 33 21.194 18.071 26.166 1LIG1 H14 34 21.426 18.051 26.275 1LIG1 H15 35 21.406 18.104 25.832 1LIG1 H16 36 21.161 17.849 26.184 1LIG1 H17 37 21.400 17.826 26.302 1LIG1 H18 38 21.392 18.152 25.676 1LIG1 H19 39 21.266 17.900 26.171 1LIG1 H20 40 21.402 17.992 25.553 1LIG1 H21 41 21.497 17.969 25.371 1LIG1 H22 42 21.350 18.020 25.620 1LIG1 H23 43 21.430 17.992 25.406 1LIG1 H24 44 21.250 18.003 25.474 1LIG1 H25 45 21.652 17.989 25.292 1LIG1 H1 46 21.383 18.272 26.305 1LIG1 H2 47 21.480 18.482 25.942 1LIG1 H3 48 21.454 18.516 26.205 1LIG1 H4 49 21.165 18.082 26.032 1LIG1 H5 50 21.550 18.035 26.221 1LIG1 H6 51 21.476 18.272 25.774 1LIG1 H7 52 21.123 17.840 26.061 1LIG1 H8 53 21.507 17.794 26.249 1LIG1 H9 54 21.568 18.105 25.633 1LIG1 H10 55 21.174 17.964 25.720 1LIG1 H11 56 21.165 17.852 25.503 1LIG1 H12 57 21.207 17.639 26.131 1LIG1 H13 58 21.269 17.788 25.324 ``` 0.00000 0.00000 0.00000 ![Screenshot from 2020-10-15 10-36-40](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/4b33e371b5f21f5f585e6d8f20629ba64af1125b.png) ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 15, 2020, 7:26am UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960/2 "2020-10-15T07:26:06Z")
Hi, The error indicates that you have a mistake in the topology. From a quick look to your lig.itp I have noticed that angle are under the section [pairs] that is wrong. Add the header [angles] before the definition of the angles. Here you can find more on the topology syntax [http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=topology%20table](http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=topology%20table) Best regards Alessandra ---
**Author:** ![swamybioinfo](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@swamybioinfo](https://gromacs.bioexcel.eu/u/swamybioinfo)\ **Post date:** [October 15, 2020, 7:30am UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960/3 "2020-10-15T07:30:22Z")
Dear Sir, please check the lig1.itp ; Created by cgenff\_charmm2gmx.py [moleculetype] ; Name nrexcl LIG1 3 [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 LIG1 rtp LIG1 q qsum 1 CG3C51 1 LIG1 C1 1 0.084 12.011 ; 2 NG3C51 1 LIG1 N1 2 -0.479 14.007 ; 3 OG311 1 LIG1 O1 3 -0.652 15.999 ; 4 CG311 1 LIG1 C2 4 -0.055 12.011 ; 5 NG311 1 LIG1 N2 5 -0.727 14.007 ; 6 OG311 1 LIG1 O2 6 -0.649 15.999 ; 7 CG3C52 1 LIG1 C3 7 0.093 12.011 ; 8 OG311 1 LIG1 O3 8 -0.617 15.999 ; 9 CG3C52 1 LIG1 C4 9 -0.212 12.011 ; 10 OG311 1 LIG1 O4 10 -0.617 15.999 ; 11 CG3C52 1 LIG1 C5 11 -0.214 12.011 ; 12 CG321 1 LIG1 C6 12 -0.168 12.011 ; 13 CG321 1 LIG1 C7 13 -0.168 12.011 ; 14 CG321 1 LIG1 C8 14 0.122 12.011 ; 15 CG321 1 LIG1 C9 15 -0.178 12.011 ; 16 CG321 1 LIG1 C10 16 -0.178 12.011 ; 17 CG311 1 LIG1 C11 17 0.006 12.011 ; 18 CG311 1 LIG1 C12 18 0.137 12.011 ; 19 CG321 1 LIG1 C13 19 -0.163 12.011 ; 20 CG311 1 LIG1 C14 20 -0.096 12.011 ; 21 CG321 1 LIG1 C15 21 -0.169 12.011 ; 22 CG311 1 LIG1 C16 22 0.138 12.011 ; 23 CG321 1 LIG1 C17 23 -0.179 12.011 ; 24 CG311 1 LIG1 C18 24 0.408 12.011 ; 25 HGA1 1 LIG1 H01 25 0.090 1.008 ; 26 HGA1 1 LIG1 H02 26 0.090 1.008 ; 27 HGPAM1 1 LIG1 H03 27 0.347 1.008 ; 28 HGA2 1 LIG1 H04 28 0.090 1.008 ; 29 HGP1 1 LIG1 H05 29 0.369 1.008 ; 30 HGA2 1 LIG1 H06 30 0.090 1.008 ; 31 HGP1 1 LIG1 H07 31 0.369 1.008 ; 32 HGA2 1 LIG1 H08 32 0.090 1.008 ; 33 HGA2 1 LIG1 H09 33 0.090 1.008 ; 34 HGA2 1 LIG1 H14 34 0.090 1.008 ; 35 HGA2 1 LIG1 H15 35 0.090 1.008 ; 36 HGA2 1 LIG1 H16 36 0.090 1.008 ; 37 HGA2 1 LIG1 H17 37 0.090 1.008 ; 38 HGA1 1 LIG1 H18 38 0.090 1.008 ; 39 HGA1 1 LIG1 H19 39 0.090 1.008 ; 40 HGA2 1 LIG1 H20 40 0.090 1.008 ; 41 HGA1 1 LIG1 H21 41 0.090 1.008 ; 42 HGA2 1 LIG1 H22 42 0.090 1.008 ; 43 HGA1 1 LIG1 H23 43 0.090 1.008 ; 44 HGA2 1 LIG1 H24 44 0.090 1.008 ; 45 HGA1 1 LIG1 H25 45 0.090 1.008 ; 46 HGA2 1 LIG1 H1 46 0.090 1.008 ; 47 HGA2 1 LIG1 H2 47 0.090 1.008 ; 48 HGA2 1 LIG1 H3 48 0.090 1.008 ; 49 HGA2 1 LIG1 H4 49 0.090 1.008 ; 50 HGA2 1 LIG1 H5 50 0.090 1.008 ; 51 HGA2 1 LIG1 H6 51 0.090 1.008 ; 52 HGA2 1 LIG1 H7 52 0.090 1.008 ; 53 HGA2 1 LIG1 H8 53 0.090 1.008 ; 54 HGA2 1 LIG1 H9 54 0.090 1.008 ; 55 HGA2 1 LIG1 H10 55 0.090 1.008 ; 56 HGA2 1 LIG1 H11 56 0.090 1.008 ; 57 HGP1 1 LIG1 H12 57 0.419 1.008 ; 58 HGP1 1 LIG1 H13 58 0.419 1.008 ; [bonds] ; ai aj funct c0 c1 c3 1 2 1 1 9 1 1 14 1 1 25 1 2 4 1 2 7 1 3 57 1 3 18 1 4 12 1 4 13 1 4 26 1 5 14 1 5 27 1 5 17 1 6 58 1 6 22 1 7 11 1 7 28 1 7 46 1 8 24 1 8 29 1 9 11 1 9 30 1 9 47 1 10 24 1 10 31 1 11 32 1 11 48 1 12 15 1 12 33 1 12 49 1 13 16 1 13 34 1 13 50 1 14 35 1 14 51 1 15 18 1 15 36 1 15 52 1 16 18 1 16 37 1 16 53 1 17 19 1 17 21 1 17 38 1 18 39 1 19 20 1 19 40 1 19 54 1 20 22 1 20 24 1 20 41 1 21 23 1 21 42 1 21 55 1 22 23 1 22 43 1 23 44 1 23 56 1 24 45 1 [pairs] ; ai aj funct c0 c1 c2 c3 1 12 1 1 13 1 1 26 1 1 28 1 1 46 1 1 27 1 1 17 1 1 32 1 1 48 1 2 30 1 2 47 1 2 5 1 2 35 1 2 51 1 2 15 1 2 33 1 2 49 1 2 16 1 2 34 1 2 50 1 2 32 1 2 48 1 3 12 1 3 36 1 3 52 1 3 13 1 3 37 1 3 53 1 4 9 1 4 14 1 4 25 1 4 11 1 4 28 1 4 46 1 4 18 1 4 36 1 4 52 1 4 37 1 4 53 1 5 9 1 5 25 1 5 20 1 5 40 1 5 54 1 5 23 1 5 42 1 5 55 1 6 19 1 6 24 1 6 41 1 6 21 1 6 44 1 6 56 1 7 14 1 7 25 1 7 12 1 7 13 1 7 26 1 7 30 1 7 47 1 8 31 1 8 19 1 8 22 1 8 41 1 9 35 1 9 51 1 9 28 1 9 46 1 10 29 1 10 19 1 10 22 1 10 41 1 11 14 1 11 25 1 12 16 1 12 34 1 12 50 1 12 39 1 13 15 1 13 33 1 13 49 1 13 39 1 14 30 1 14 47 1 14 19 1 14 21 1 14 38 1 15 57 1 15 26 1 15 37 1 15 53 1 16 57 1 16 26 1 16 36 1 16 52 1 17 35 1 17 51 1 17 22 1 17 24 1 17 41 1 17 44 1 17 56 1 18 33 1 18 49 1 18 34 1 18 50 1 19 27 1 19 23 1 19 42 1 19 55 1 19 43 1 19 45 1 20 58 1 20 29 1 20 31 1 20 21 1 20 38 1 20 44 1 20 56 1 21 27 1 21 40 1 21 54 1 21 43 1 22 40 1 22 54 1 22 45 1 22 42 1 22 55 1 23 58 1 23 38 1 23 24 1 23 41 1 24 40 1 24 54 1 24 43 1 25 30 1 25 47 1 25 35 1 25 51 1 26 33 1 26 49 1 26 34 1 26 50 1 27 35 1 27 51 1 27 38 1 28 32 1 28 48 1 29 45 1 30 32 1 30 48 1 31 45 1 32 46 1 32 47 1 33 36 1 33 52 1 34 37 1 34 53 1 36 49 1 36 39 1 37 50 1 37 39 1 38 40 1 38 54 1 38 42 1 38 55 1 39 57 1 39 52 1 39 53 1 40 41 1 41 54 1 41 43 1 41 45 1 42 44 1 42 56 1 43 58 1 43 44 1 43 56 1 44 55 1 46 48 1 47 48 1 49 52 1 50 53 1 55 56 1 [angles] ; ai aj ak funct c0 c1 c2 c3 2 1 9 5 ; NG3C51 CG3C51 CG3C52 2 1 14 5 ; NG3C51 CG3C51 CG321 2 1 25 5 ; NG3C51 CG3C51 HGA1 9 1 14 5 ; CG3C52 CG3C51 CG321 9 1 25 5 ; CG3C52 CG3C51 HGA1 14 1 25 5 ; CG321 CG3C51 HGA1 1 2 4 5 ; CG3C51 NG3C51 CG311 1 2 7 5 ; CG3C51 NG3C51 CG3C52 4 2 7 5 ; CG311 NG3C51 CG3C52 57 3 18 5 ; HGP1 OG311 CG311 2 4 12 5 ; NG3C51 CG311 CG321 2 4 13 5 ; NG3C51 CG311 CG321 2 4 26 5 ; NG3C51 CG311 HGA1 12 4 13 5 ; CG321 CG311 CG321 12 4 26 5 ; CG321 CG311 HGA1 13 4 26 5 ; CG321 CG311 HGA1 14 5 27 5 ; CG321 NG311 HGPAM1 14 5 17 5 ; CG321 NG311 CG311 27 5 17 5 ; HGPAM1 NG311 CG311 58 6 22 5 ; HGP1 OG311 CG311 2 7 11 5 ; NG3C51 CG3C52 CG3C52 2 7 28 5 ; NG3C51 CG3C52 HGA2 2 7 46 5 ; NG3C51 CG3C52 HGA2 11 7 28 5 ; CG3C52 CG3C52 HGA2 11 7 46 5 ; CG3C52 CG3C52 HGA2 28 7 46 5 ; HGA2 CG3C52 HGA2 24 8 29 5 ; CG311 OG311 HGP1 1 9 11 5 ; CG3C51 CG3C52 CG3C52 1 9 30 5 ; CG3C51 CG3C52 HGA2 1 9 47 5 ; CG3C51 CG3C52 HGA2 11 9 30 5 ; CG3C52 CG3C52 HGA2 11 9 47 5 ; CG3C52 CG3C52 HGA2 30 9 47 5 ; HGA2 CG3C52 HGA2 24 10 31 5 ; CG311 OG311 HGP1 7 11 9 5 ; CG3C52 CG3C52 CG3C52 7 11 32 5 ; CG3C52 CG3C52 HGA2 7 11 48 5 ; CG3C52 CG3C52 HGA2 9 11 32 5 ; CG3C52 CG3C52 HGA2 9 11 48 5 ; CG3C52 CG3C52 HGA2 32 11 48 5 ; HGA2 CG3C52 HGA2 4 12 15 5 ; CG311 CG321 CG321 4 12 33 5 ; CG311 CG321 HGA2 4 12 49 5 ; CG311 CG321 HGA2 15 12 33 5 ; CG321 CG321 HGA2 15 12 49 5 ; CG321 CG321 HGA2 33 12 49 5 ; HGA2 CG321 HGA2 4 13 16 5 ; CG311 CG321 CG321 4 13 34 5 ; CG311 CG321 HGA2 4 13 50 5 ; CG311 CG321 HGA2 16 13 34 5 ; CG321 CG321 HGA2 16 13 50 5 ; CG321 CG321 HGA2 34 13 50 5 ; HGA2 CG321 HGA2 1 14 5 5 ; CG3C51 CG321 NG311 1 14 35 5 ; CG3C51 CG321 HGA2 1 14 51 5 ; CG3C51 CG321 HGA2 5 14 35 5 ; NG311 CG321 HGA2 5 14 51 5 ; NG311 CG321 HGA2 35 14 51 5 ; HGA2 CG321 HGA2 12 15 18 5 ; CG321 CG321 CG311 12 15 36 5 ; CG321 CG321 HGA2 12 15 52 5 ; CG321 CG321 HGA2 18 15 36 5 ; CG311 CG321 HGA2 18 15 52 5 ; CG311 CG321 HGA2 36 15 52 5 ; HGA2 CG321 HGA2 13 16 18 5 ; CG321 CG321 CG311 13 16 37 5 ; CG321 CG321 HGA2 13 16 53 5 ; CG321 CG321 HGA2 18 16 37 5 ; CG311 CG321 HGA2 18 16 53 5 ; CG311 CG321 HGA2 37 16 53 5 ; HGA2 CG321 HGA2 5 17 19 5 ; NG311 CG311 CG321 5 17 21 5 ; NG311 CG311 CG321 5 17 38 5 ; NG311 CG311 HGA1 19 17 21 5 ; CG321 CG311 CG321 19 17 38 5 ; CG321 CG311 HGA1 21 17 38 5 ; CG321 CG311 HGA1 3 18 15 5 ; OG311 CG311 CG321 3 18 16 5 ; OG311 CG311 CG321 3 18 39 5 ; OG311 CG311 HGA1 15 18 16 5 ; CG321 CG311 CG321 15 18 39 5 ; CG321 CG311 HGA1 16 18 39 5 ; CG321 CG311 HGA1 17 19 20 5 ; CG311 CG321 CG311 17 19 40 5 ; CG311 CG321 HGA2 17 19 54 5 ; CG311 CG321 HGA2 20 19 40 5 ; CG311 CG321 HGA2 20 19 54 5 ; CG311 CG321 HGA2 40 19 54 5 ; HGA2 CG321 HGA2 19 20 22 5 ; CG321 CG311 CG311 19 20 24 5 ; CG321 CG311 CG311 19 20 41 5 ; CG321 CG311 HGA1 22 20 24 5 ; CG311 CG311 CG311 22 20 41 5 ; CG311 CG311 HGA1 24 20 41 5 ; CG311 CG311 HGA1 17 21 23 5 ; CG311 CG321 CG321 17 21 42 5 ; CG311 CG321 HGA2 17 21 55 5 ; CG311 CG321 HGA2 23 21 42 5 ; CG321 CG321 HGA2 23 21 55 5 ; CG321 CG321 HGA2 42 21 55 5 ; HGA2 CG321 HGA2 6 22 20 5 ; OG311 CG311 CG311 6 22 23 5 ; OG311 CG311 CG321 6 22 43 5 ; OG311 CG311 HGA1 20 22 23 5 ; CG311 CG311 CG321 20 22 43 5 ; CG311 CG311 HGA1 23 22 43 5 ; CG321 CG311 HGA1 21 23 22 5 ; CG321 CG321 CG311 21 23 44 5 ; CG321 CG321 HGA2 21 23 56 5 ; CG321 CG321 HGA2 22 23 44 5 ; CG311 CG321 HGA2 22 23 56 5 ; CG311 CG321 HGA2 44 23 56 5 ; HGA2 CG321 HGA2 8 24 10 5 ; OG311 CG311 OG311 8 24 20 5 ; OG311 CG311 CG311 8 24 45 5 ; OG311 CG311 HGA1 10 24 20 5 ; OG311 CG311 CG311 10 24 45 5 ; OG311 CG311 HGA1 20 24 45 5 ; CG311 CG311 HGA1 [dihedrals] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 9 1 2 4 9 ; CG3C52 CG3C51 NG3C51 CG311 9 1 2 7 9 ; CG3C52 CG3C51 NG3C51 CG3C52 14 1 2 4 9 ; CG321 CG3C51 NG3C51 CG311 14 1 2 7 9 ; CG321 CG3C51 NG3C51 CG3C52 25 1 2 4 9 ; HGA1 CG3C51 NG3C51 CG311 25 1 2 7 9 ; HGA1 CG3C51 NG3C51 CG3C52 2 1 9 11 9 ; NG3C51 CG3C51 CG3C52 CG3C52 2 1 9 30 9 ; NG3C51 CG3C51 CG3C52 HGA2 2 1 9 47 9 ; NG3C51 CG3C51 CG3C52 HGA2 14 1 9 11 9 ; CG321 CG3C51 CG3C52 CG3C52 14 1 9 30 9 ; CG321 CG3C51 CG3C52 HGA2 14 1 9 47 9 ; CG321 CG3C51 CG3C52 HGA2 25 1 9 11 9 ; HGA1 CG3C51 CG3C52 CG3C52 25 1 9 30 9 ; HGA1 CG3C51 CG3C52 HGA2 25 1 9 47 9 ; HGA1 CG3C51 CG3C52 HGA2 2 1 14 5 9 ; NG3C51 CG3C51 CG321 NG311 2 1 14 35 9 ; NG3C51 CG3C51 CG321 HGA2 2 1 14 51 9 ; NG3C51 CG3C51 CG321 HGA2 9 1 14 5 9 ; CG3C52 CG3C51 CG321 NG311 9 1 14 35 9 ; CG3C52 CG3C51 CG321 HGA2 9 1 14 51 9 ; CG3C52 CG3C51 CG321 HGA2 25 1 14 5 9 ; HGA1 CG3C51 CG321 NG311 25 1 14 35 9 ; HGA1 CG3C51 CG321 HGA2 25 1 14 51 9 ; HGA1 CG3C51 CG321 HGA2 1 2 4 12 9 ; CG3C51 NG3C51 CG311 CG321 1 2 4 13 9 ; CG3C51 NG3C51 CG311 CG321 1 2 4 26 9 ; CG3C51 NG3C51 CG311 HGA1 7 2 4 12 9 ; CG3C52 NG3C51 CG311 CG321 7 2 4 13 9 ; CG3C52 NG3C51 CG311 CG321 7 2 4 26 9 ; CG3C52 NG3C51 CG311 HGA1 1 2 7 11 9 ; CG3C51 NG3C51 CG3C52 CG3C52 1 2 7 28 9 ; CG3C51 NG3C51 CG3C52 HGA2 1 2 7 46 9 ; CG3C51 NG3C51 CG3C52 HGA2 4 2 7 11 9 ; CG311 NG3C51 CG3C52 CG3C52 4 2 7 28 9 ; CG311 NG3C51 CG3C52 HGA2 4 2 7 46 9 ; CG311 NG3C51 CG3C52 HGA2 57 3 18 15 9 ; HGP1 OG311 CG311 CG321 57 3 18 16 9 ; HGP1 OG311 CG311 CG321 57 3 18 39 9 ; HGP1 OG311 CG311 HGA1 2 4 12 15 9 ; NG3C51 CG311 CG321 CG321 2 4 12 33 9 ; NG3C51 CG311 CG321 HGA2 2 4 12 49 9 ; NG3C51 CG311 CG321 HGA2 13 4 12 15 9 ; CG321 CG311 CG321 CG321 13 4 12 33 9 ; CG321 CG311 CG321 HGA2 13 4 12 49 9 ; CG321 CG311 CG321 HGA2 26 4 12 15 9 ; HGA1 CG311 CG321 CG321 26 4 12 33 9 ; HGA1 CG311 CG321 HGA2 26 4 12 49 9 ; HGA1 CG311 CG321 HGA2 2 4 13 16 9 ; NG3C51 CG311 CG321 CG321 2 4 13 34 9 ; NG3C51 CG311 CG321 HGA2 2 4 13 50 9 ; NG3C51 CG311 CG321 HGA2 12 4 13 16 9 ; CG321 CG311 CG321 CG321 12 4 13 34 9 ; CG321 CG311 CG321 HGA2 12 4 13 50 9 ; CG321 CG311 CG321 HGA2 26 4 13 16 9 ; HGA1 CG311 CG321 CG321 26 4 13 34 9 ; HGA1 CG311 CG321 HGA2 26 4 13 50 9 ; HGA1 CG311 CG321 HGA2 27 5 14 1 9 ; HGPAM1 NG311 CG321 CG3C51 27 5 14 35 9 ; HGPAM1 NG311 CG321 HGA2 27 5 14 51 9 ; HGPAM1 NG311 CG321 HGA2 17 5 14 1 9 ; CG311 NG311 CG321 CG3C51 17 5 14 35 9 ; CG311 NG311 CG321 HGA2 17 5 14 51 9 ; CG311 NG311 CG321 HGA2 14 5 17 19 9 ; CG321 NG311 CG311 CG321 14 5 17 21 9 ; CG321 NG311 CG311 CG321 14 5 17 38 9 ; CG321 NG311 CG311 HGA1 27 5 17 19 9 ; HGPAM1 NG311 CG311 CG321 27 5 17 21 9 ; HGPAM1 NG311 CG311 CG321 27 5 17 38 9 ; HGPAM1 NG311 CG311 HGA1 58 6 22 20 9 ; HGP1 OG311 CG311 CG311 58 6 22 23 9 ; HGP1 OG311 CG311 CG321 58 6 22 43 9 ; HGP1 OG311 CG311 HGA1 2 7 11 9 9 ; NG3C51 CG3C52 CG3C52 CG3C52 2 7 11 32 9 ; NG3C51 CG3C52 CG3C52 HGA2 2 7 11 48 9 ; NG3C51 CG3C52 CG3C52 HGA2 28 7 11 9 9 ; HGA2 CG3C52 CG3C52 CG3C52 28 7 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2 28 7 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2 46 7 11 9 9 ; HGA2 CG3C52 CG3C52 CG3C52 46 7 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2 46 7 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2 29 8 24 10 9 ; HGP1 OG311 CG311 OG311 29 8 24 20 9 ; HGP1 OG311 CG311 CG311 29 8 24 45 9 ; HGP1 OG311 CG311 HGA1 1 9 11 7 9 ; CG3C51 CG3C52 CG3C52 CG3C52 1 9 11 32 9 ; CG3C51 CG3C52 CG3C52 HGA2 1 9 11 48 9 ; CG3C51 CG3C52 CG3C52 HGA2 30 9 11 7 9 ; HGA2 CG3C52 CG3C52 CG3C52 30 9 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2 30 9 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2 47 9 11 7 9 ; HGA2 CG3C52 CG3C52 CG3C52 47 9 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2 47 9 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2 31 10 24 8 9 ; HGP1 OG311 CG311 OG311 31 10 24 20 9 ; HGP1 OG311 CG311 CG311 31 10 24 45 9 ; HGP1 OG311 CG311 HGA1 4 12 15 18 9 ; CG311 CG321 CG321 CG311 4 12 15 36 9 ; CG311 CG321 CG321 HGA2 4 12 15 52 9 ; CG311 CG321 CG321 HGA2 33 12 15 18 9 ; HGA2 CG321 CG321 CG311 33 12 15 36 9 ; HGA2 CG321 CG321 HGA2 33 12 15 52 9 ; HGA2 CG321 CG321 HGA2 49 12 15 18 9 ; HGA2 CG321 CG321 CG311 49 12 15 36 9 ; HGA2 CG321 CG321 HGA2 49 12 15 52 9 ; HGA2 CG321 CG321 HGA2 4 13 16 18 9 ; CG311 CG321 CG321 CG311 4 13 16 37 9 ; CG311 CG321 CG321 HGA2 4 13 16 53 9 ; CG311 CG321 CG321 HGA2 34 13 16 18 9 ; HGA2 CG321 CG321 CG311 34 13 16 37 9 ; HGA2 CG321 CG321 HGA2 34 13 16 53 9 ; HGA2 CG321 CG321 HGA2 50 13 16 18 9 ; HGA2 CG321 CG321 CG311 50 13 16 37 9 ; HGA2 CG321 CG321 HGA2 50 13 16 53 9 ; HGA2 CG321 CG321 HGA2 12 15 18 3 9 ; CG321 CG321 CG311 OG311 12 15 18 16 9 ; CG321 CG321 CG311 CG321 12 15 18 39 9 ; CG321 CG321 CG311 HGA1 36 15 18 3 9 ; HGA2 CG321 CG311 OG311 36 15 18 16 9 ; HGA2 CG321 CG311 CG321 36 15 18 39 9 ; HGA2 CG321 CG311 HGA1 52 15 18 3 9 ; HGA2 CG321 CG311 OG311 52 15 18 16 9 ; HGA2 CG321 CG311 CG321 52 15 18 39 9 ; HGA2 CG321 CG311 HGA1 13 16 18 3 9 ; CG321 CG321 CG311 OG311 13 16 18 15 9 ; CG321 CG321 CG311 CG321 13 16 18 39 9 ; CG321 CG321 CG311 HGA1 37 16 18 3 9 ; HGA2 CG321 CG311 OG311 37 16 18 15 9 ; HGA2 CG321 CG311 CG321 37 16 18 39 9 ; HGA2 CG321 CG311 HGA1 53 16 18 3 9 ; HGA2 CG321 CG311 OG311 53 16 18 15 9 ; HGA2 CG321 CG311 CG321 53 16 18 39 9 ; HGA2 CG321 CG311 HGA1 5 17 19 20 9 ; NG311 CG311 CG321 CG311 5 17 19 40 9 ; NG311 CG311 CG321 HGA2 5 17 19 54 9 ; NG311 CG311 CG321 HGA2 21 17 19 20 9 ; CG321 CG311 CG321 CG311 21 17 19 40 9 ; CG321 CG311 CG321 HGA2 21 17 19 54 9 ; CG321 CG311 CG321 HGA2 38 17 19 20 9 ; HGA1 CG311 CG321 CG311 38 17 19 40 9 ; HGA1 CG311 CG321 HGA2 38 17 19 54 9 ; HGA1 CG311 CG321 HGA2 5 17 21 23 9 ; NG311 CG311 CG321 CG321 5 17 21 42 9 ; NG311 CG311 CG321 HGA2 5 17 21 55 9 ; NG311 CG311 CG321 HGA2 19 17 21 23 9 ; CG321 CG311 CG321 CG321 19 17 21 42 9 ; CG321 CG311 CG321 HGA2 19 17 21 55 9 ; CG321 CG311 CG321 HGA2 38 17 21 23 9 ; HGA1 CG311 CG321 CG321 38 17 21 42 9 ; HGA1 CG311 CG321 HGA2 38 17 21 55 9 ; HGA1 CG311 CG321 HGA2 17 19 20 22 9 ; CG311 CG321 CG311 CG311 17 19 20 24 9 ; CG311 CG321 CG311 CG311 17 19 20 41 9 ; CG311 CG321 CG311 HGA1 40 19 20 22 9 ; HGA2 CG321 CG311 CG311 40 19 20 24 9 ; HGA2 CG321 CG311 CG311 40 19 20 41 9 ; HGA2 CG321 CG311 HGA1 54 19 20 22 9 ; HGA2 CG321 CG311 CG311 54 19 20 24 9 ; HGA2 CG321 CG311 CG311 54 19 20 41 9 ; HGA2 CG321 CG311 HGA1 19 20 22 6 9 ; CG321 CG311 CG311 OG311 19 20 22 23 9 ; CG321 CG311 CG311 CG321 19 20 22 43 9 ; CG321 CG311 CG311 HGA1 24 20 22 6 9 ; CG311 CG311 CG311 OG311 24 20 22 23 9 ; CG311 CG311 CG311 CG321 24 20 22 43 9 ; CG311 CG311 CG311 HGA1 41 20 22 6 9 ; HGA1 CG311 CG311 OG311 41 20 22 23 9 ; HGA1 CG311 CG311 CG321 41 20 22 43 9 ; HGA1 CG311 CG311 HGA1 19 20 24 8 9 ; CG321 CG311 CG311 OG311 19 20 24 10 9 ; CG321 CG311 CG311 OG311 19 20 24 45 9 ; CG321 CG311 CG311 HGA1 22 20 24 8 9 ; CG311 CG311 CG311 OG311 22 20 24 10 9 ; CG311 CG311 CG311 OG311 22 20 24 45 9 ; CG311 CG311 CG311 HGA1 41 20 24 8 9 ; HGA1 CG311 CG311 OG311 41 20 24 10 9 ; HGA1 CG311 CG311 OG311 41 20 24 45 9 ; HGA1 CG311 CG311 HGA1 17 21 23 22 9 ; CG311 CG321 CG321 CG311 17 21 23 44 9 ; CG311 CG321 CG321 HGA2 17 21 23 56 9 ; CG311 CG321 CG321 HGA2 42 21 23 22 9 ; HGA2 CG321 CG321 CG311 42 21 23 44 9 ; HGA2 CG321 CG321 HGA2 42 21 23 56 9 ; HGA2 CG321 CG321 HGA2 55 21 23 22 9 ; HGA2 CG321 CG321 CG311 55 21 23 44 9 ; HGA2 CG321 CG321 HGA2 55 21 23 56 9 ; HGA2 CG321 CG321 HGA2 6 22 23 21 9 ; OG311 CG311 CG321 CG321 6 22 23 44 9 ; OG311 CG311 CG321 HGA2 6 22 23 56 9 ; OG311 CG311 CG321 HGA2 20 22 23 21 9 ; CG311 CG311 CG321 CG321 20 22 23 44 9 ; CG311 CG311 CG321 HGA2 20 22 23 56 9 ; CG311 CG311 CG321 HGA2 43 22 23 21 9 ; HGA1 CG311 CG321 CG321 43 22 23 44 9 ; HGA1 CG311 CG321 HGA2 43 22 23 56 9 ; HGA1 CG311 CG321 HGA2 ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 15, 2020, 7:39am UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960/4 "2020-10-15T07:39:58Z")
Hi again, what are exactly the errors when you run grompp without the option -maxwarn ? I have also noticed that the last line of lig.gro is 0.000 0.000 0.000, did you put the molecule in the box ? Best regards Alessandra ---
**Author:** ![swamybioinfo](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@swamybioinfo](https://gromacs.bioexcel.eu/u/swamybioinfo)\ **Post date:** [October 15, 2020, 8:21am UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960/5 "2020-10-15T08:21:52Z")
Dear Sir, I have created the lig.gro from the commands python3 cgenff\_charmm2gmx\_py3\_nx2.py LIG lig1\_fix.mol2 lig.str charmm36-mar2019.ff gmx editconf -f lig\_ini.pdb -o lig.gro gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0 gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr i am getting same error. as Fatal error: Invalid bond type 0 I am confused where is error.? After generation of lig.gro i found all box vectors are 0 0 0. please check the images for lig.gro and protein.pro and coplex.gro for box vectors box vectros as per protein.gro 1147SER OT116459 21.272 21.779 11.587 1147SER OT216460 21.297 21.808 11.627 8.23623 11.58355 16.02296 box vectors as per lig.gro 1LIG1 H12 57 21.207 17.639 26.131 1LIG1 H13 58 21.269 17.788 25.324 0.00000 0.00000 0.00000 Complex.gro box vectors 1LIG1 H12 57 21.207 17.639 26.131 1LIG1 H13 58 21.269 17.788 25.324 0.00000 0.00000 0.00000 8.23623 11.58355 16.02296 0.00000 0.00000 0.00000 later i followed the steps as per tutorial > **[Protein-Ligand Complex](http://www.mdtutorials.com/gmx/complex/02_topology.html)** ![Screenshot from 2020-10-15 13-35-13](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/478ae146c9e7b82bae9cf795eac40ecc68157504.png) ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [October 16, 2020, 2:10am UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960/6 "2020-10-16T02:10:33Z")
What does your `.top` file contain? ---
**Author:** ![swamybioinfo](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@swamybioinfo](https://gromacs.bioexcel.eu/u/swamybioinfo)\ **Post date:** [October 16, 2020, 4:56pm UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960/7 "2020-10-16T16:56:14Z")
16459 OC 1147 SER OT1 16459 -0.67 15.9994 16460 OC 1147 SER OT2 16460 -0.67 15.9994 ; qtot -7 [bonds] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 5 11 1 7 8 1 7 9 1 7 10 1 11 12 1 11 13 1 13 14 1 13 15 1 15 16 1 15 17 1 15 32 1 17 18 1 17 19 1 17 20 1 20 21 1 20 28 1 21 22 1 21 23 1 23 24 1 23 25 1 25 26 1 ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [October 18, 2020, 9:48pm UTC](https://gromacs.bioexcel.eu/t/grompp-fatal-error-invalid-bond-type/960/8 "2020-10-18T21:48:35Z")
That is not your `.top` file contents.