# CG Simulation error **URL:** \ **Category:** User discussions\ **Created:** [December 6, 2024, 5:07am UTC](https://gromacs.bioexcel.eu/t/cg-simulation-error/10736 "2024-12-06T05:07:51Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Sonia](https://avatars.discourse-cdn.com/v4/letter/s/c67d28/32.png) [@Sonia](https://gromacs.bioexcel.eu/u/Sonia)\ **Post date:** [December 6, 2024, 5:07am UTC](https://gromacs.bioexcel.eu/t/cg-simulation-error/10736/1 "2024-12-06T05:07:52Z")
GROMACS version:2022 GROMACS modification: Yes/No Here post your question I am trying to run the command for CG MD simulation of graphene: gmx\_mpi grompp -f minim.mdp -c system.gro -r system.gro -p topol.top -o em.tpr but I am getting the error: Atomtype CG2R61 not found I have generated the structure and obtained forcefield and .itp files from CHARMM-GUI, I do not get how to solve this error. Can someone please help? ---
**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\ **Post date:** [December 6, 2024, 11:28am UTC](https://gromacs.bioexcel.eu/t/cg-simulation-error/10736/2 "2024-12-06T11:28:34Z")
Are you sure this is a CG MD? The atomtype you described is an all-atom atom for carbon nanoparticles. Regarding the error, check the following: 1. You are using the force field files obtained from C-GUI. These are usually in the toppar folder. 2. topol.top has #include blocks. Verify the path of force field files is correct. I have run multiple graphene and CNT simulations using input files generated by C-GUI without this error. ---
**Author:** ![Sonia](https://avatars.discourse-cdn.com/v4/letter/s/c67d28/32.png) [@Sonia](https://gromacs.bioexcel.eu/u/Sonia)\ **Post date:** [December 6, 2024, 11:52am UTC](https://gromacs.bioexcel.eu/t/cg-simulation-error/10736/3 "2024-12-06T11:52:36Z")
I have generated the all-atom pdb structure from charmm-gui which i further want to use in cg simulation. The CG pdb structure I have made using CGBuilder tool in VMD, for which I go the .apr, .top, and .pdb files but I am getting this Atomtype error and also few additional ones. So, if you could kindly suggest how to proceed or resolve this, it would be of great help. Thank You. ---
**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\ **Post date:** [December 6, 2024, 5:10pm UTC](https://gromacs.bioexcel.eu/t/cg-simulation-error/10736/4 "2024-12-06T17:10:38Z")
Which CG force field do you intend to use? If it is Martini FF, the atomtype (actually, beadtype) will be C1, SC1 or something else based on the AA-to-CG mapping, functional groups, etc. There are many reports on 3-to-1 and 4-to-1 mapping schemes where 3 or 4 carbons are mapped to a single CG bead. I haven’t worked on other CG FF so can’t comment on those. ---
**Author:** ![Sonia](https://avatars.discourse-cdn.com/v4/letter/s/c67d28/32.png) [@Sonia](https://gromacs.bioexcel.eu/u/Sonia)\ **Post date:** [December 7, 2024, 4:45am UTC](https://gromacs.bioexcel.eu/t/cg-simulation-error/10736/5 "2024-12-07T04:45:10Z")
Yes I am using the Martini FF. I will check if these atomtype works. Thank you ---
**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\ **Post date:** [December 7, 2024, 8:34am UTC](https://gromacs.bioexcel.eu/t/cg-simulation-error/10736/6 "2024-12-07T08:34:58Z")
Things are not that simple. The bonded parameters (bonds lengths, bond angles, etc.) will change. So, just replacing atomtype wouldn’t suffice. I would suggest go through the literature troghly for your specific end use. For example, Titov (2010) and Shih (2015) both use a 3-to-1 mapping but SC4 and SC3 beads, respectively. Also look Wallace (2007) which uses 4-to-1 mapping. There is still no consensus which model best describes graphene. But looking at Martini guidelines, I suggest that you go for a 3-to-1 mapping with small beads. There is also a CNP bead described by Luca Monticelli which may be adapted in your study. But note that the arrangement of small beadtypes won’t, typically, be in a hexagon but in triangles. ---
**Author:** ![Sonia](https://avatars.discourse-cdn.com/v4/letter/s/c67d28/32.png) [@Sonia](https://gromacs.bioexcel.eu/u/Sonia)\ **Post date:** [December 7, 2024, 9:24am UTC](https://gromacs.bioexcel.eu/t/cg-simulation-error/10736/7 "2024-12-07T09:24:51Z")
Noted with thanks. I have been going through and making certain changes but still getting the error of Atomtype 1 not found