How to md simulation of organic molecule in acetone

User discussions
1

Dear Sir,
I hope this message finds you well. I am reaching out to seek assistance regarding an error I encountered while attempting to run a molecular dynamics (MD) simulation. I am conducting simulations of an organic molecule in an acetone solvent using GROMACS, with force fields derived from CHARMM for the solvent and AMBER antechamber for the organic molecule.
Upon attempting to run the simulation, I encountered the following error message:

Fatal error:
Syntax error - File charmm36.itp, line 12
Last line read:
‘[ atomtypes ]’
Invalid order for directive atomtypes
"

I have attached a link to my Google Drive containing all the relevant files, including the final topology file named “acetoneandmolecule.top”.
https://drive.google.com/drive/folders/13TY6R9eQFG1yQm1hJcEMBbHcZTsW3W08
Could you kindly review the files and advise on how to resolve this issue? Additionally, if the steps I’ve followed thus far are incorrect, I would greatly appreciate your guidance on the correct procedure.

Looking forward to your guidance.

Best regards,
LUKHMANUL HAKEEM K.

2

You need to include the aceton topology as itp file. not as top file

3

Dear Sir,
I already run the calculation by including acetone topology file as 'ACTO.itp" then I got error like this
“ERROR 1 [file ACTO.itp, line 7]:
Atomtype OG2D3 not found” So that’s why I inculde “.top” file. Please help me to resolve this issue.
Best regards,
LUKHMANUL HAKEEM K.

4

I cannot acess your files,
You need to keep the solute topology in .top file and insert the itp file right after the solute topology. BTW, you cannnot mix two force field, that will lead to unphysical simulations.

5

Dear Sir,
Now the problem has been solved. Thank you for your help.

Best reagards,
LUKHMANUL HAKEEM K.