# Fatal error: No line with moleculetype 'SOL' found the \[ molecules \] section of file 'complex.top'

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-the-molecules-section-of-file-complex-top/12981>\
**Category:** User discussions\
**Tags:** simulation-setup\
**Created:** [November 28, 2025, 7:19am UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-the-molecules-section-of-file-complex-top/12981 "2025-11-28T07:19:53Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![bfopoku](https://avatars.discourse-cdn.com/v4/letter/b/2acd7d/32.png) [@bfopoku](https://gromacs.bioexcel.eu/u/bfopoku)\
**Post date:** [November 28, 2025, 7:19am UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-the-molecules-section-of-file-complex-top/12981/1 "2025-11-28T07:19:53Z")

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GROMACS version: version 2021.4-Ubuntu-2021.4-2  
GROMACS modification: Yes/No  
Hello everyone i’m a new user on GROMACS and i’ve been trying my hands on ligand-protein complex. i’ve gotten to the point i balance the charges in my system after ions addition. the prompt after selecting SOL issues a fatal errorr; Fatal error: No line with moleculetype ‘SOL’ found the [molecules] section of file ‘complex.top’. I would be grateful if anyone could show me how to resolve this. FYI my GROMACS is compiles in a Linux compartment and i run it from a WSL on my windows computer. here’s the relevant part of my complex.top file that has the SOL

; Include Position restraint file  
#ifdef POSRES  
#include “posre.itp”  
#endif

; Include water topology  
#include “charmm36.ff/tip3p.itp”

#ifdef POSRES\_WATER  
; Position restraint for each water oxygen  
[position\_restraints]  
; i funct fcx fcy fcz  
1 1 1000 1000 1000  
#endif

; Include topology for ions  
#include “charmm36.ff/ions.itp”

[system]  
; Name  
Protein

[molecules]  
; Compound #mols  
Protein\_chain\_A 1  
lig 1  
SOL 32661

here’s the command together with user inputs that generated this error

gmx genion -s ions.tpr -o solv\_ions.gro -p complex.top -pname NA -nname CL -neutral

Reading file ions.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)  
Reading file ions.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)  
Will try to add 31 NA ions and 0 CL ions.  
Select a continuous group of solvent molecules  
Group 0 ( System) has 109084 elements  
Group 1 ( Protein) has 11035 elements  
Group 2 ( Protein-H) has 5530 elements  
Group 3 ( C-alpha) has 718 elements  
Group 4 ( Backbone) has 2154 elements  
Group 5 ( MainChain) has 2871 elements  
Group 6 ( MainChain+Cb) has 3535 elements  
Group 7 ( MainChain+H) has 3555 elements  
Group 8 ( SideChain) has 7480 elements  
Group 9 ( SideChain-H) has 2659 elements  
Group 10 ( Prot-Masses) has 11035 elements  
Group 11 ( non-Protein) has 98049 elements  
Group 12 ( Other) has 66 elements  
Group 13 ( MOL) has 66 elements  
Group 14 ( Water) has 97983 elements  
Group 15 ( SOL) has 97983 elements  
Group 16 ( non-Water) has 11101 elements  
Select a group: 15  
Selected 15: ‘SOL’  
Number of (3-atomic) solvent molecules: 32661

Processing topology

* * *

Program: gmx genion, version 2021.4-Ubuntu-2021.4-2  
Source file: src/gromacs/gmxpreprocess/genion.cpp (line 351)

Fatal error:  
No line with moleculetype ‘SOL’ found the [molecules] section of file  
‘complex.top’

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [November 28, 2025, 4:21pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-the-molecules-section-of-file-complex-top/12981/2 "2025-11-28T16:21:27Z")

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There does seem to be a line with SOL in the molecules section. Maybe there is no newline at the end of this line?

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<div class="post-metadata">

**Author:** ![bfopoku](https://avatars.discourse-cdn.com/v4/letter/b/2acd7d/32.png) [@bfopoku](https://gromacs.bioexcel.eu/u/bfopoku)\
**Post date:** [November 29, 2025, 4:24am UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-the-molecules-section-of-file-complex-top/12981/3 "2025-11-29T04:24:27Z")

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thank you for the response. i ran a dos2unix on my complex.top file as jalemkul from [thelemkullab.com](http://www.thelemkullab.com/) recommended to another user and it worked.