Home
Keywords
News
Edit
History
Recent changes
New version:
Cuby4
documentation
is here
QMMM tutorial
New name
Password
Show page
Syntax
!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 preparaton 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}}
Password
Edit summary