Hi everyone,

I'm currently working on preparing a carbon dot system (~1482 atoms) for molecular dynamics simulations using the CHARMM force field. However, I’ve run into an issue during the parameterization step.

I initially tried using CGenFF, but the process failed likely due to the large number of atoms in the structure. I then attempted to process the system through CHARMM-GUI, but received the following error:

“There is a mismatch in the order of ligand heavy atoms between the SDF/MOL2 file and the original PDB file.”

The attached file illustrates the mismatch error I encountered.

I would greatly appreciate any guidance on how to resolve this.

Are there alternative tools or workflows you’d recommend for parameterizing large carbon-based nanostructures using CHARMM force fields?

Thank you in advance for your help!