# MD simulation using gromacs of Protein Ligand complex with Two Hematoms of NDP & UNK

**URL:** <https://gromacs.bioexcel.eu/t/md-simulation-using-gromacs-of-protein-ligand-complex-with-two-hematoms-of-ndp-unk/9293>\
**Category:** User discussions\
**Tags:** forcefield, mdrun\
**Created:** [June 4, 2024, 4:11am UTC](https://gromacs.bioexcel.eu/t/md-simulation-using-gromacs-of-protein-ligand-complex-with-two-hematoms-of-ndp-unk/9293 "2024-06-04T04:11:22Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Rubha](https://avatars.discourse-cdn.com/v4/letter/r/b2d939/32.png) [@Rubha](https://gromacs.bioexcel.eu/u/Rubha)\
**Post date:** [June 4, 2024, 4:11am UTC](https://gromacs.bioexcel.eu/t/md-simulation-using-gromacs-of-protein-ligand-complex-with-two-hematoms-of-ndp-unk/9293/1 "2024-06-04T04:11:22Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

While perform Protein ligand MD simulation i am getting error “Atom P1 in residue NDP 193 was not found in rtp entry NDP with 75 atoms  
while sorting atoms” after performing pdbtogmx command, Kindly help me to rectify this error

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**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [June 5, 2024, 8:15am UTC](https://gromacs.bioexcel.eu/t/md-simulation-using-gromacs-of-protein-ligand-complex-with-two-hematoms-of-ndp-unk/9293/2 "2024-06-05T08:15:01Z")

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It’s saying there’s an issue with your coordinate file, that the atom P1 of residue NDP 193 in your file shouldn’t be there.