Simulated ligand with weird geometries on start.pdb(dump=0) and md_0_100.gro files

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GROMACS version:2021.4-Ubuntu
GROMACS modification: Yes/No
Here post your question:

I run 100nsec simulation with all ‘default’ parameter suggested by the tutorial Protein-Ligand Complex. After 10 days the simulation was finally over. To visualize the results prior to the analysis step, i uploaded into Pymol start.pdb(dump0) and md_0_100.gro. What I saw was that the ligand had wrong geometries for the Oxetane(left on the image) and Trifluoro (right on the image). I was planning to run Hbond and RMSD analysis but I dont know if I can trust the results. Thoughts?
image

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PyMOL is guessing bonds from interatomic distances. It will certainly guess the oxetane wrong; it even does this with histidine sometimes. The trifluoro group does not look like it has F atoms; those look to be H based on default coloring. But even if they are F, the same comment applies. PyMOL is just confused.

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Thanks for your quick response. I opened the ligand in another tool and both the Oxetane and Trifluoro look normal, as you suggested. I would like to few screen shots for my publication. Is there a way to correct this?

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You can delete incorrect bonds. Refer to the PyMOL documentation and seek guidance from their help forum if you need it.

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