# Distortion of cyclopeptide during energy minimization **URL:** \ **Category:** User discussions\ **Created:** [January 3, 2025, 3:56pm UTC](https://gromacs.bioexcel.eu/t/distortion-of-cyclopeptide-during-energy-minimization/10938 "2025-01-03T15:56:33Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![mohsen](https://avatars.discourse-cdn.com/v4/letter/m/8491ac/32.png) [@mohsen](https://gromacs.bioexcel.eu/u/mohsen)\ **Post date:** [January 3, 2025, 3:56pm UTC](https://gromacs.bioexcel.eu/t/distortion-of-cyclopeptide-during-energy-minimization/10938/1 "2025-01-03T15:56:34Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hi everyone I am trying to use MD simulation to evaluate the interaction between cyclopeptide and one ligand . I want to have a planar shape of cyclopeptide and i have to mention that at first my structure optimized using DFT method…however,at the energy minimization step, my cyclopeptide got twisted and lost its planner shape…i tried dihedral restrain but it didn’t work…what should i do? ---
**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:** [January 3, 2025, 4:12pm UTC](https://gromacs.bioexcel.eu/t/distortion-of-cyclopeptide-during-energy-minimization/10938/2 "2025-01-03T16:12:55Z")
How many residues are in your cyclic peptide? Are the amino acids a mixture of D- and L-stereoisomers or are they all one chirality? If the latter, it should not stay planar. ---
**Author:** ![mohsen](https://avatars.discourse-cdn.com/v4/letter/m/8491ac/32.png) [@mohsen](https://gromacs.bioexcel.eu/u/mohsen)\ **Post date:** [January 3, 2025, 4:22pm UTC](https://gromacs.bioexcel.eu/t/distortion-of-cyclopeptide-during-energy-minimization/10938/3 "2025-01-03T16:22:26Z")
Thank you for your answer dear @jalemkul It contains 12 residues yes it consists of alternating L and D isomers, but i dont realize why it lost its planar structure ---
**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:** [January 5, 2025, 4:01am UTC](https://gromacs.bioexcel.eu/t/distortion-of-cyclopeptide-during-energy-minimization/10938/4 "2025-01-05T04:01:19Z")
What force field are you using? None of the common biomolecular force fields aim to reproduce DFT generally, so this could just be a mismatch between what the QM and MM are expected to produce. ---
**Author:** ![mohsen](https://avatars.discourse-cdn.com/v4/letter/m/8491ac/32.png) [@mohsen](https://gromacs.bioexcel.eu/u/mohsen)\ **Post date:** [January 5, 2025, 6:22am UTC](https://gromacs.bioexcel.eu/t/distortion-of-cyclopeptide-during-energy-minimization/10938/5 "2025-01-05T06:22:00Z")
I am using CHARMM36 OK,Thanks for your reply @jalemkul ---
**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:** [January 5, 2025, 7:51pm UTC](https://gromacs.bioexcel.eu/t/distortion-of-cyclopeptide-during-energy-minimization/10938/6 "2025-01-05T19:51:51Z")
Right, CHARMM is parametrized against MP2/6-31+G\* optimized geometries so that’s what you should use to compare. We don’t target polypeptides of any sort generally but the energy surfaces associated with (φ,ψ) rotation. ---
**Author:** ![mohsen](https://avatars.discourse-cdn.com/v4/letter/m/8491ac/32.png) [@mohsen](https://gromacs.bioexcel.eu/u/mohsen)\ **Post date:** [January 6, 2025, 2:04pm UTC](https://gromacs.bioexcel.eu/t/distortion-of-cyclopeptide-during-energy-minimization/10938/7 "2025-01-06T14:04:26Z")
Alright, now i see Thanks,dear @jalemkul, for taking the time