# Qmmm preparation basic

One of major required pieces of information that has to be provided in the prepare block for QM/MM simulations is the definition of the QM region. This can be accomplished using modify directive used either per atom

modify atom <integer isgm>:<string atomname> quantum


or per segment/residue basis

modify segment <integer isgm> quantum


Here isgm and atomname refer to the residue number and atom name record as given in the PDB file. It is important to note that that the leading blanks in atom name record should be indicated with underscores. Per PDB format guidelines the atom name record starts at column 13. If, for example, the atom name record “OW” starts in the 14th column in PDB file, it will appear as “_OW” in the modify atom directive in the prepare block.

In the current implementation only solute atoms can be declared as quantum. If part of the solvent has to be treated quantum mechanically then it has to redeclared to be solute. The definition of QM region should be accompanied by update lists and ignore directives. Here is an example input file that will generate QM/MM restart and topology files for the ethanol molecule:

title "Prepare QM/MM calculation of ethanol"
start etl

[prepare](Prepare)
#--*name of the pdbfile*
source [etl0.pdb](etl0.pdb)
#--*generate new topology and sequence file*
new_top new_seq
#--*generate new restart file*
new_rst
#--*define quantum region (note the use of underscore)*
modify atom 1:_C1  quantum
modify atom 1:2H1  quantum
modify atom 1:3H1  quantum
modify atom 1:4H1  quantum
update lists
ignore
#--*save restart file*
write etl_ref.rst
#--*generate pdb file*
write [etl_ref.pdb](etl_ref.pdb)
end