GROMACS version: 2020.2
GROMACS modification: Yes/No
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I am facing a problem with cGenff, my compound is a spiro type and in this way not supported from cGenfF. Is it any other option to generate correct topology for spiro compounds or how to run. I tried MD gromacs with spiro compound but was aborted during the energy minimization, whereas when I tried another compound (not spiro) it worked correctly.
If atom types or other aspects of the parameters are not supported, you will have to manually parametrize the molecule, including potentially introducing a new atom type. This can be very laborious.
Is it the issue that cGenff does not support spiro compounds or Gromacs, because if is the problem of cGenff it would be solved by using another topology creator tool available and supported by Gromacs.
Thank you for your readiness.
You said in your first post that CGenFF didn’t support some necessary atom type, so I’m assuming that’s your issue. If there’s something else going on, you need to be more clear about the actual problem. GROMACS isn’t linked to any specific force field or topology generation program; it will accept any viable topology, even one you write entirely by hand.
When I upload my compound to cGenff it says: Attype warning spiro compound not explicitly
Then you’ve answered your question: CGenFF doesn’t support your molecule and therefore you cannot generate a topology for it, for GROMACS or any other software. You will need to either manually parametrize it or use a different force field that does support such species.