Dear Gromacs user,
I’m involved in making a box including graphene sheets, protein and water.
I made the topology file for Graphene using x2top command creating a new file in charm36.ff, called graphene.n2t. The .top file was made successfully. But when I was using grommp command in order to make .tpr file, I received this message that
CR1 atom not defined.
CR1 is graphene carbon atom which was defined in .n2t file
I’m wondering how I can solve this fatal error .
Thanks,
CR1 is a GROMOS atom type, not CHARMM. The error suggests you’re trying to combine multiple force fields, which is not appropriate.
[quote=“azshamlou, post:3, topic:1904, full:true”]
Thank you for your response.
It seems unusual since I made the .top file correctly and the Atomtype was found in the forcefield. However while using Grompp command, Gromacs checked for the second time the force field and can not find the Atomtype.
Do you have any idea why I got this error?
I appreciate your help in advance.
Thanks
You can specify whatever you like in the .n2t file, but we do not distribute one with the CHARMM36 port so either you made it yourself with a nonexistent atom type (you can check yourself in atomtypes.atp, there’s no CR1 there) or you obtained an .n2t file from another source that was designed for use with a different force field. Regardless, the answer is the same. You’re using an invalid atom type, which x2top knows nothing about. It does what you tell it. grompp will let you know if you were wrong :)
What is the basis for selecting parameters for graphene sheet for charm ff?
As with any force field, identifying the most chemically appropriate atom type. For graphene, my first guess would be CA for CHARMM, since that is the stock aromatic carbon type.