I am trying to visualize the 2D interaction between ligand and protein from a PDB file I extracted from the MD simulation trajectory. But I get the error "Ligand is not a single fragment".
probably The extra bonds suggest that your bond lengths are too short.
Sometimes, this is seen if a 2D sdf has been download instead of the energy-minimised 3D sdf file.
Sudarshan Lamichhane
This post discussed a similar issue. Hope it helps.
https://www.researchgate.net/post/Ligand_is_not_s_single_fragment_on_BIOVIA_discovery_studio_What_do
Check the structure again!
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