# Fatal error: No line with moleculetype 'SOL' found but it is present in topol.top

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-but-it-is-present-in-topol-top/5817>\
**Category:** User discussions\
**Created:** [February 16, 2023, 9:40pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-but-it-is-present-in-topol-top/5817 "2023-02-16T21:40:18Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Hanoriega](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hanoriega/32/1562_2.png) [@Hanoriega](https://gromacs.bioexcel.eu/u/Hanoriega)\
**Post date:** [February 16, 2023, 9:40pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-but-it-is-present-in-topol-top/5817/1 "2023-02-16T21:40:18Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

Hello,

I am running into this error and don’t quite understand. I am trying to neutralize my system and there is definitely a SOL moleculetype at the bottom of the topol.top file. How do I fix this?

Program: gmx genion, version 2022.5  
Source file: src/gromacs/gmxpreprocess/genion.cpp (line 351)

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

THIS IS THE MOLECULES SECTION FROM THE TOPOL.TOP

[molecules]  
; Compound #mols  
Protein\_chain\_A 1  
Protein\_chain\_B 1  
Protein\_chain\_C 1  
Protein\_chain\_D 1  
Protein\_chain\_E 1  
Protein\_chain\_F 1  
Protein\_chain\_G 1  
Protein\_chain\_H 1  
Protein\_chain\_I 1  
Protein\_chain\_J 1  
Protein\_chain\_K 1  
Protein\_chain\_L 1  
Protein\_chain\_M 1  
Protein\_chain\_N 1  
Protein\_chain\_O 1  
Protein\_chain\_P 1  
Protein\_chain\_Q 1  
Protein\_chain\_R 1  
Protein\_chain\_S 1  
Protein\_chain\_T 1  
Protein\_chain\_U 1  
Protein\_chain\_V 1  
Protein\_chain\_W 1  
Protein\_chain\_X 1  
Protein\_chain\_Y 1  
Protein\_chain\_Z 1  
Protein\_chain\_a 1  
Protein\_chain\_b 1  
Protein\_chain\_c 1  
Protein\_chain\_d 1  
Protein\_chain\_e 1  
Protein\_chain\_f 1  
Protein\_chain\_g 1  
Protein\_chain\_h 1  
Protein\_chain\_i 1  
Protein\_chain\_j 1  
Protein\_chain\_k 1  
Protein\_chain\_l 1  
Protein\_chain\_m 1  
Protein\_chain\_n 1  
Protein\_chain\_o 1  
Protein\_chain\_p 1  
Protein\_chain\_q 1  
Protein\_chain\_r 1  
Protein\_chain\_s 1  
Protein\_chain\_t 1  
Protein\_chain\_u 1  
Protein\_chain\_v 1  
Protein\_chain\_w 1  
Protein\_chain\_x 1  
Protein\_chain\_y 1  
Protein\_chain\_z 1  
Protein\_chain\_1 1  
Protein\_chain\_2 1  
Protein\_chain\_3 1  
Protein\_chain\_4 1  
Protein\_chain\_5 1  
Protein\_chain\_6 1  
Protein\_chain\_7 1  
Protein\_chain\_8 1  
SOL 876467

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<div class="post-metadata">

**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:** [February 17, 2023, 2:59pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-but-it-is-present-in-topol-top/5817/2 "2023-02-17T14:59:28Z")

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Hi,  
You could provide some extra information.  
how is your command line? did you use the option -p to provide the correct name of your topology to gmx genion ?  
Kind regards  
\Alessandra

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<div class="post-metadata">

**Author:** ![Hanoriega](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hanoriega/32/1562_2.png) [@Hanoriega](https://gromacs.bioexcel.eu/u/Hanoriega)\
**Post date:** [February 17, 2023, 4:19pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-but-it-is-present-in-topol-top/5817/3 "2023-02-17T16:19:20Z")

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Hello,

Yes so command line is:

gmx genion -s ions.tpr -o solvate\_ions.gro -conc 0.15 -p topol.top -pname NA -nname CL -neutral

Then I select 13-SOL

Then that error appears. However when I search in the topol.top file it has the SOL line shown like above. There is a #topol.top.1# that is backed up with no SOL, but I am confused.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [February 17, 2023, 5:16pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-but-it-is-present-in-topol-top/5817/4 "2023-02-17T17:16:28Z")

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The most likely cause of the issue is the presence of a non-\*nix style line ending on the SOL line, implying the file was once opened with a non-plain text editor. Run dos2unix on `topol.top` and then try again.

> [@Hanoriega](#):
>
> There is a #topol.top.1# that is backed up with no SOL, but I am confused.

The purpose of `genion` is to modify the topology. GROMACS always writes these types of backup file instead of overwriting one with the same name, so you can recover your work if something goes wrong.

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<div class="post-metadata">

**Author:** ![Hanoriega](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hanoriega/32/1562_2.png) [@Hanoriega](https://gromacs.bioexcel.eu/u/Hanoriega)\
**Post date:** [February 17, 2023, 5:28pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-no-line-with-moleculetype-sol-found-but-it-is-present-in-topol-top/5817/5 "2023-02-17T17:28:54Z")

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ok, thank you both.