Issue in Generating topology file

User discussions
1

GROMACS version:2022
GROMACS modification: Yes/No
Here post your question
I am trying to generate topology for graphene and graphene oxide using CGenff but the str file does not generate any details of it and also i am getting this error: Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (3021) and top (0) are unequal
Usually this means the specified residue name does not match between str and mol2 files
How to resolve this?
the str file has this:

  • Toppar stream file generated by
  • CHARMM General Force Field (CGenFF) program version 4.0
  • For use with CGenFF version 4.6

read rtf card append

  • Topologies generated by
  • CHARMM General Force Field (CGenFF) program version 4.0

36 1

! “penalty” is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

END

read param card flex append

  • Parameters generated by analogy by
  • CHARMM General Force Field (CGenFF) program version 4.0

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

BONDS

ANGLES

DIHEDRALS

IMPROPERS

END
RETURN

2

There is nothing in the stream file so there’s nothing to convert. CGenFF is not suitable for something like graphene; all the atom types are the same (aromatic carbon) and charges are all zero. The GROMACS x2top program is probably more suitable for generating this kind of topology.

3

Thank you for the reply. Could you kindly elaborate/share more on this x2top program?

4

It would be better to look at the literature to see how these structures are paramterised, for example in this we have provided the parameters for rGO, you may able to use or produce in the same way, if that is suitable for your forcefield.