Ligand Topology Issue?

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Ricardo J Ferreira

Which software are you using?

Suraj Chougula

Ricardo J Ferreira, I am using Gromacs for MD simulation. After performing docking using Auto Dock Vina, I separated the ligand from the protein for topology generation. Still, I am facing the problem of nitrogen with four bonds in the separated ligand. How do I resolve this while preserving the co-ordinates?

And which force field? CHARMM or AMBER?

Ricardo J Ferreira i generated the topology but i have another error in the nvt step where it is saying that there are clashes in the complex.gro file and potential energy is extremely high.