GROMACS version: 2021.4
GROMACS modification: Yes
Dear GROMACS users,
I’m trying simulate a polymeric matrix composed by lignin + PLA system with charmm36 force field.
I generated the GROMACS files with charmm2gmx. And there is a problem when I used the ‘gmx grompp’.
The command line below:
gmx grompp -f minim-2.mdp -c syr_box.gro -p topol.top o minim.tpr
When I run the command line occur this error:
ERROR 1 [file ffbonded.itp, line 25]:
Unknown bond_atomtype CC3151
If somebody have any idea to solve this error? Thank you for reply
CC3151 is a standard carbohydrate atom type. Did you generate the entire force field yourself? That’s not necessary; the latest CHARMM toppar files were ported to GROMACS format last year and are available from Alex MacKerell’s website. If you aren’t use those files, you should. How did you generate the lignin topology?
Thank you so much for your reply.
I used the “Systematic parameterization of lignin for the CHARMM force field” made by Vermass et,al; 2018 and then convert into a GROMACS format using the charmm2gmx tool.
To clarify, are you converting the entire CHARMM force field with our charmm2gmx program (which isn’t necessary, we’ve already done that for you) or some standalone topology?
You are right, I see that CHARMM toppar files for lignin already exist.
Thank you so much for your reply it was helpful.