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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?
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.
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
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.
I am using CHARMM36
OK,Thanks for your reply @jalemkul
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.
Alright, now i see
Thanks,dear @jalemkul, for taking the time