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!WORK IN PROGRESS In this tutorial we will prepare QM/MM calculation of a peptide where one amino acid (tryptofan) sidechain is calculated at QM level. AMBER is used for the MM calculation, DFTB for QM. The preparation of the MM calculation is specific for AMBER, but DFTB can be replaced with any other QM method. !! Files Tryptofan cage miniprotein is used. PDB ready for AMBER calculation is available [here]. !! Forcefield preparation The MM calculation of the whole peptide will run as it is. To perform the calculation on the QM region, we have to prepare residue for the sidechain. Firstly, wee need to determine the bond length for the link atom in the QM method we will use. The sidechain can be selected and saved using the [geometry] script: {{geometry -s ':TRP&%not(%atomname(N,H,HA,C,O))' trpcage.pdb > selection.pdb}} In the file, we replace the C alpha: {{ATOM 128 CA TRP 9 0.273 2.606 -0.574}} with hydrogen link atom {{ATOM 128 HL TRP 9 0.273 2.606 -0.574}} For further use, we also rename the residue "TRP" in this file to "trp". To optimize the bond length, we prepare following input (opt_link.yaml): {{interface: dftb charge: 0 freeze_atoms: "%not(1)" # Only the first atom in the geometry is optimized restart_file: optimized_link.xyz # default setup is used for the optimization}} and run the optimization: {{cuby_optimize opt_link.yaml selection.pdb}} Now, we measure the optimized bond length on the resulting structure (optimized_link.xyz); it is 1.10 A. !! Forcefield preparation - AMBER specific In xleap !! Not covered here Multiple residues in pdb - adding TERs
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