Marek
Freindorf
Q-Chem Workshop
Examples Part 4
University of North Texas
August 2011
CH2O-H2O Calculations
QM/MM Method
QM
QM
The CH2O and H2O
hydrogen bonded
complex
Page 2
QM/MM Method
CH2O-H2O Calculations
Full geometry
optimization
using the
B3LYP/6-31+G*
level of theory
Page 3
QM/MM Method
CH2O-H2O Calculations
The final energy
of the dimer
Page 4
QM/MM Method
CH2O-H2O Calculations
Atomic charges
from the
B3LYP/6-31+G*
level of theory
Page 5
CH2O-H2O Calculations
QM/MM Method
QM
MM
The CH2O and H2O
hydrogen bonded
complex
Page 6
QM/MM Method
CH2O-H2O Calculations
The input file for the
QM/MM calculation
The coordinates of the
QM molecule
Full geometry
optimization using the
B3LYP/6-31+G* level
of theory
The keywords which
keep the QM molecule
at its original orientation
Page 7
QM/MM Method
CH2O-H2O Calculations
The external
charges and
the LennardJones
parameters of
the MM atoms
The LennardJones
parameters of
the QM atoms
Page 8
QM/MM Method
CH2O-H2O Calculations
The MM external charges and
Lennard-Jones parameters of water
atoms from AMBER
The MM external charges and their LJ
parameters depend on a particular MM force
field used in the calculations
Page 9
QM/MM Method
CH2O-H2O Calculations
The Lennard-Jones parameters of the
QM atoms depend on a particular QM
level of theory used in the QM/MM
calculations
Practically the LJ parameters of the
QM atoms are about 20% bigger than
corresponding LJ parameters of those
atoms in molecular mechanics
Page 10
QM/MM Method
CH2O-H2O Calculations
The output from the QM/MM
calculation
The energy components of
the QM/MM interaction
Page 11
QM/MM Method
CH2O-H2O Calculations
The final total energy of the QM/MM system
after geometry optimization
Page 12
QM/MM Method
CH2O-H2O Calculations
Atomic charges of the QM
atoms after geometry optimization
in a presence of the external MM
atoms
Page 13
QM/MM Method
C2H5NH2-PROTEIN Calculations
The ligand geometry taken
from the “pcaf-qm.xyz” file
Do not “Translate to the
center”
Page 14
QM/MM Method
C2H5NH2-PROTEIN Calculations
Seup the QM/MM
input file by selecting
“QChem Setup”
Page 15
QM/MM Method
C2H5NH2-PROTEIN Calculations
The absolute
values of the xyz
coordinates
Geometry
optimization at the
B2LYP/6-31+G*
level of theory
Keywords keeping
the QM molecule
at its original
orientation
Page 16
QM/MM Method
C2H5NH2-PROTEIN Calculations
In the “Advanced”
window, select the
“QM/MM” option
Page 17
QM/MM Method
C2H5NH2-PROTEIN Calculations
Select the “Read
Charges” option
Page 18
QM/MM Method
C2H5NH2-PROTEIN Calculations
Select the file with
MM charges
Page 19
QM/MM Method
C2H5NH2-PROTEIN Calculations
The MM
charges and
their LJ
parameters of
the QM system
They have to be
read from a
corresponding
disk file
Page 20
QM/MM Method
C2H5NH2-PROTEIN Calculations
The LJ parameters
of the QM atoms
They are
automatically
generated by the
QUI program
Page 21
QM/MM Method
C2H5NH2-PROTEIN Calculations
The final QM coordinates after geometry
optimization
The final total energy of the system
(QM + MM)
Page 22
QM/MM Method
C2H5NH2-PROTEIN Calculations
The energy of the interaction between the
MM atoms
The final total energy includes the interaction
energy between the MM atoms
Page 23
QM/MM Method
C2H5NH2-PROTEIN Calculations
The final charges of
the QM system,
based on the
Mulliken population
The final QM dipole
moment
Page 24
QM/MM Method
Protein
C2H5NH2-PROTEIN Calculations
Gas Phase
The final energy after
The final energy in the
excluding the MM
gas phase
interaction energy
∆E = -10.9 kcal/mol
Page 25
QM/MM Method
Protein
C2H5NH2-PROTEIN Calculations
Gas Phase
Page 26
QM/MM Method
C2H5NH2-PROTEIN Vibrations
The final coordinates of
the ligand after
geometry optimization
in the protein
The frequency
calculations of the
ligand in the protein
Page 27
QM/MM Method
C2H5NH2-PROTEIN Vibrations
The geometry of the ligand is
in the global minimum in the
protein
Page 28
QM/MM Method
Protein
C2H5NH2-PROTEIN Vibrations
Gas Phase
Page 29
QM/MM Method
C2H5NH2-PROTEIN Vibrations
Protein
Gas Phase
Page 30
QM/MM Method
Chair-PROTEIN Calculations
The geometry of the
ligand taken from the
“renin-qm.xyz” files
Do not “Translate
the center”
Page 31
QM/MM Method
Chair-PROTEIN Calculations
Setup the QM/MM
input file by
selecting “QChem
Setup”
Page 32
QM/MM Method
Chair-PROTEIN Calculations
The absolute values of the
ligand coordinates
The full geometry optimization
for the fixed initial orientation
of the ligand
Page 33
QM/MM Method
Chair-PROTEIN Calculations
Read MM charges from
the “renin-mm.chg” file
Page 34
QM/MM Method
Chair-PROTEIN Calculations
The fixed absolute
position of the first
atom of the ligand
This atom was
originally connected
to the protein
External charges of the MM system
(the protein) read from a disk file
Page 35
QM/MM Method
Chair-PROTEIN Calculations
The Lennard-Jones
parameters, which
are automatically
generated by the
QUI editor
Page 36
QM/MM Method
Chair-PROTEIN Calculations
The final
coordinates of the
ligand after
geometry
optimization in the
protein
The final total
energy of the
system, including
the MM interaction
energies
Page 37
QM/MM Method
Chair-PROTEIN Calculations
The final charges
of the ligand in the
protein
Page 38