When creating a Graphene layer in VMD using the Nanotube Builder it only generates hexagons with single bonds because of this errors occur when creating the topology for gromacs software using, graphene with double bonds

gmx x2top -f graphene.pdb -o system.top

Here are the errors observed in gromacs output

Can not find forcefield for atom C-4 with 3 bonds
Can not find forcefield for atom C-6 with 3 bonds
Can not find forcefield for atom C-7 with 3 bonds
Can not find forcefield for atom C-8 with 3 bonds

Please not that the border line C atoms will assign H atoms this can be done with another software which is not the major issue its missing double bonds thus carbon is missing its full 4 bonds.

Can anyone help me with this issue or please suggest any other software that can do this.

  • 2
    $\begingroup$ Have you also used the TopoTools plugin to add bond information? From the VMD page for the Nanotube/Graphene builder: "The plugin itself only computes the carbon atom positions according to the provided input, but then has the option to generate further topology information suitable for classical force field MD simulations, which can then be stored in files of a suitable format. This uses functionality provided by the TopoTools plugin..." $\endgroup$
    – Tyberius
    Nov 10, 2021 at 15:22
  • 2
    $\begingroup$ Maybe hte tutorial of Andrea Minoia can help, it has example x2top files and you might only need an xyz file of the CNT, not a pdb: chembytes.wikidot.com/grocnt#toc1 $\endgroup$
    – Orr22
    Nov 14, 2021 at 18:16
  • $\begingroup$ This question appears to be abandoned. It can be reopened if the OP addresses questions/suggestions in the comments or anyone else wants to give an answer. $\endgroup$
    – Tyberius
    Jan 14, 2022 at 2:27


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