# No such moleculetype 'SOL'

**URL:** <https://gromacs.bioexcel.eu/t/no-such-moleculetype-sol/10475>\
**Category:** User discussions\
**Created:** [November 4, 2024, 6:44am UTC](https://gromacs.bioexcel.eu/t/no-such-moleculetype-sol/10475 "2024-11-04T06:44:43Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Nish\_asin](https://avatars.discourse-cdn.com/v4/letter/n/94ad74/32.png) [@Nish\_asin](https://gromacs.bioexcel.eu/u/Nish_asin)\
**Post date:** [November 4, 2024, 6:44am UTC](https://gromacs.bioexcel.eu/t/no-such-moleculetype-sol/10475/1 "2024-11-04T06:44:43Z")

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GROMACS version: 2021.4-Ubuntu-2021.4-2  
GROMACS modification: Yes/No  
Here post your question :  
Hello everyone,  
I am currently working on solvating my Chitosan-Dextran Aldehyde copolymer and I’m running into some issues. I executed the following command to perform the solvation:  
“gmx solvate -cp out.gro -cs tip4p.gro -o solvated.gro -p CHI\_DexAld\_5\_GMX.top”

To provide some context, I used Material Studio to build the polymer, and since `pdb2gmx` was not compatible with my polymer structure, I utilized ACPYPE to generate the necessary files (like .itp, .gro, .top, etc.) for GROMACS simulations.

However, after the solvation stage, I keep encountering this error when I try to run the command:  
“gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o ions.tpr”

The error:  
“ERROR 1 [file CHI\_DexAld\_5\_GMX.top, line 22]:  
No such moleculetype SOL”  
In my `CHI_DexAld_5_GMX.top` file, I have the following lines:  
“; Compound nmols  
CHI\_DexAld\_5 1  
SOL 3024”  
I also made sure to include the line `#include "tip4p.itp"` in the topology file. Despite these efforts, I’m still facing the same issue. I even tried using different water models, like `spc216.gro`, but with no success.

I would greatly appreciate any guidance or insights you might have to help me resolve this issue :(

I can also provide necessary informations if anyone want.  
Thank you in advance.

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 4, 2024, 10:46am UTC](https://gromacs.bioexcel.eu/t/no-such-moleculetype-sol/10475/2 "2024-11-04T10:46:47Z")

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Hi,  
Could you upload your topology (CHI\_DexAld\_5\_GMX.top) somewhere and make it available for downloading? That would help finding what the issue might be.

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<div class="post-metadata">

**Author:** ![Nish\_asin](https://avatars.discourse-cdn.com/v4/letter/n/94ad74/32.png) [@Nish\_asin](https://gromacs.bioexcel.eu/u/Nish_asin)\
**Post date:** [November 4, 2024, 2:57pm UTC](https://gromacs.bioexcel.eu/t/no-such-moleculetype-sol/10475/5 "2024-11-04T14:57:39Z")

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This is the onedrive link for my CHI\_DexAld\_5\_GMX.top file:  
[CHI\_DexAld\_5\_GMX.top](https://buetedu-my.sharepoint.com/:u:/g/personal/1918006_bme_buet_ac_bd/EdxF51jCkgNPlwMIR7LiNkwB1S3B557_PiLR4olQ8J4R7w?e=1dYSRJ)

You can download it if you want. Thank you for your help.

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**Author:** ![Nish\_asin](https://avatars.discourse-cdn.com/v4/letter/n/94ad74/32.png) [@Nish\_asin](https://gromacs.bioexcel.eu/u/Nish_asin)\
**Post date:** [November 5, 2024, 3:47am UTC](https://gromacs.bioexcel.eu/t/no-such-moleculetype-sol/10475/6 "2024-11-05T03:47:07Z")

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Here is the Google Drive link to my topology file for your reference:

> **[CHI\_DexAld\_5\_GMX.top](https://drive.google.com/file/d/1egattkzaBuPElUyFG4HKA-mOf1YabCoq/view?usp=sharing)**
>
> Google Drive file.

I apologize for the multiple replies; as this is my first time posting here, I initially didn’t realize that Akismet temporarily hides posts.  
Any insights or help will be appreciated.  
Thanks

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**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [November 5, 2024, 11:04am UTC](https://gromacs.bioexcel.eu/t/no-such-moleculetype-sol/10475/7 "2024-11-05T11:04:51Z")

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Dear @Nish_asin

I think this might be your problem :)

```auto
#ifdef POSRES_LIG
#include "posre_CHI_DexAld_5.itp"
#include "tip4p.itp" ; <------ here

#endif

```

You are including the topology for water inside the `#ifdef -- #endif` section, so if you do not require the restraints you lose the topology. Try with this and see if this fixes the problem

```auto
#ifdef POSRES_LIG
#include "posre_CHI_DexAld_5.itp"
#endif
#include "tip4p.itp" ; <------ moved outside

```

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<div class="post-metadata">

**Author:** ![Nish\_asin](https://avatars.discourse-cdn.com/v4/letter/n/94ad74/32.png) [@Nish\_asin](https://gromacs.bioexcel.eu/u/Nish_asin)\
**Post date:** [November 8, 2024, 6:56am UTC](https://gromacs.bioexcel.eu/t/no-such-moleculetype-sol/10475/8 "2024-11-08T06:56:51Z")

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Dear @obZehn,  
Thank you for your response. I did the change as you suggested. But then it was showing error like:  
ERROR 1 [file tip4p.itp, line 7]:  
Atomtype OW\_tip4p not found

From what I understood, the `tip4p.itp` water model file wasn’t included in the force field being used by the `grompp` command(likely amber). I attempted to switch to alternative water models (`spc.itp` and `tip3p.itp`), but both returned similar errors.  
I noticed that ACPYPE generated an additional topology file, `CHI_DexAld_5_GMX_OPLS.top`, alongside `CHI_DexAld_5_GMX.top`. I decided to try using this OPLS topology file and made the required modifications as you advised. Also in the "CHI\_DexAld\_5\_GMX\_OPLS.top’ file I have to include the line:  
#include “oplsaa.ff/forcefield.itp”

And it worked!!  
Thank you so much for your help!

Regards,  
Nishat