No such moleculetype 'SOL'

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1

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.

2

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.

5

This is the onedrive link for my CHI_DexAld_5_GMX.top file:
CHI_DexAld_5_GMX.top

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

6

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

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

7

Dear @Nish_asin

I think this might be your problem :)

#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

#ifdef POSRES_LIG
#include "posre_CHI_DexAld_5.itp"
#endif
#include "tip4p.itp"                          ; <------ moved outside
8

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