# Simulated ligand with weird geometries on start.pdb(dump=0) and md\_0\_100.gro files

**URL:** <https://gromacs.bioexcel.eu/t/simulated-ligand-with-weird-geometries-on-start-pdb-dump-0-and-md-0-100-gro-files/7651>\
**Category:** User discussions\
**Tags:** mdrun, analysis-tools\
**Created:** [November 15, 2023, 2:24pm UTC](https://gromacs.bioexcel.eu/t/simulated-ligand-with-weird-geometries-on-start-pdb-dump-0-and-md-0-100-gro-files/7651 "2023-11-15T14:24:44Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sshechte1](https://avatars.discourse-cdn.com/v4/letter/s/c4cdca/32.png) [@sshechte1](https://gromacs.bioexcel.eu/u/sshechte1)\
**Post date:** [November 15, 2023, 2:24pm UTC](https://gromacs.bioexcel.eu/t/simulated-ligand-with-weird-geometries-on-start-pdb-dump-0-and-md-0-100-gro-files/7651/1 "2023-11-15T14:24:44Z")

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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](http://www.mdtutorials.com/gmx/complex/09_analysis.html). 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](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/2/2252e3e212a6e2413ad9bd8024262ba79e0a95f1.png)

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [November 15, 2023, 4:49pm UTC](https://gromacs.bioexcel.eu/t/simulated-ligand-with-weird-geometries-on-start-pdb-dump-0-and-md-0-100-gro-files/7651/2 "2023-11-15T16:49:32Z")

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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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**Author:** ![sshechte1](https://avatars.discourse-cdn.com/v4/letter/s/c4cdca/32.png) [@sshechte1](https://gromacs.bioexcel.eu/u/sshechte1)\
**Post date:** [November 15, 2023, 5:34pm UTC](https://gromacs.bioexcel.eu/t/simulated-ligand-with-weird-geometries-on-start-pdb-dump-0-and-md-0-100-gro-files/7651/3 "2023-11-15T17:34:16Z")

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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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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [November 15, 2023, 5:45pm UTC](https://gromacs.bioexcel.eu/t/simulated-ligand-with-weird-geometries-on-start-pdb-dump-0-and-md-0-100-gro-files/7651/4 "2023-11-15T17:45:17Z")

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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.