wmcsameeragroup/pyqmmm

Python interface for subtractive QM/MM calculations with AMOEBA polarizable force field using Gaussian16 and Tinker.

PyQMMM

Python interface for subtractive QM/MM calculations with AMOEBA polarizable force field (PyQM/MM) interfaces between Gaussian16 and Tinker programs. PyQM/MM does not require third-party Python packages and therefore works with the default Python installation in the system (version 3.6 or higher).
Once Gaussian executes an ONIOM(QM:MM) calculation with the keyword external, PyQM/MM converts the Gaussian16 input data (*.EIn) into Tinker compatible inputs (*.xyz) and then executes the Tinker calculation. Then, the MM data (*.epout, *.gout, *.hes) is recovered to construct a Gaussian16 compatible data source file (*.EOu) to continue the ONIOM(QM:MM) calculation. The incorporation of Tinker tools enables users to use a wide range of MM force fields such as AMOEBA, MMFF, MM3, OPLS, CHARMM, AMBER, etc.

Installation

Download the program code from https://github.com/WMCSameeraGroup/pyqmmm and extract it. (we assume that you have extracted to " ~/")

cd ~/pyqmmm
# set permissions
chmod +x pyqmmm.py

Example Calculation

PyQM/MM requires three input files and the parameter file for Tinker.

1. *.com: Gaussian input file.
2. input.key: Tinker keywords file.
3. atomtypes.dat: stores Gaussian and Tinker atom types.

Gaussian16 input

Gaussian uses the external keyword to execute external programs for ONIOM(QM:MM) calculations.

#p opt(cartesian,maxcyc=100,nomicro) freq=noraman nosymm oniom(wb97xd/6-31G*:external="/home/user/pyqmmmm/pyqmmm.py") geom=connectivity

input.key

Tinker reads input.key to locate the MM parameter file of Tinker (e.g. amoeba09.prm). Also, g16_scratch and tinker_path would be defined.

parameters /path/to/parameters/amoeba09.prm

# Define `g16_scratch` and `tinker_path`.
#----------------------------------------
g16_scratch /path/to/scratch/scr-water
tinker_path /home/useer/apps/tinker

atomtypes.dat

Tinker program needs MM atom types to calculate MM potential energy and derivatives. Therefore, Gaussian16 atom types must be converted to the corresponding Tinker atom types. The atomtypes.dat file contains both Gaussian16 and Tinker atom types.

# file: atomtypes.dat
# atomicNo   element   g16AtomType   tinkerAtomType   atomDescription
  8           O         OW            36                "Water O"
  1           H         HW            37                "Water H"

For instance, oxygen in water molecule is identified as OW in Gaussian16 and atomtype 36 in amoeba09 force field.

# file: waterbox.com
...
 O-OW--0.834000  -1   14.23459000   -1.56102400    2.67321600 L
 H-HW-0.417000   -1   13.70916000   -1.77735100    3.45832800 L
 H-HW-0.417000   -1   14.22399200   -0.58589000    2.60858200 L
...

# file: amoeba09.prm
...
atom         36   34    O     "Water O"            8    15.999    2
atom         37   35    H     "Water H"            1     1.008    1
...

Then, Gaussian16 calculation can be submitted.

Submission script:

# file: run.csh
#!/bin/csh

set INP=waterbox.com
set SCR=wat
setenv GAUSS_SCRDIR /path/to/scratch/folder/${SCR}

mkdir -p $GAUSS_SCRDIR
g16 < ${INP} > ${INP:r}.log
rm -rf $GAUSS_SCRDIR

See ./examples/water for complete set of files.