In this project I was trying to figure out distance between two ligands bounded to a phosphate backbone of DNA with highest degree of accuracy. The ligand also contains non standard elements which motivated me to use quantum forcefields instead of classical all atoms MD simulations.

  • To draw the different structures of the ligands and the DNA I use avagadro which draws them and somewhat optimizes them as well.
  • This cml files are now optimized using MMFF94s forcefield before proceeding with calculation in GAMESS, Gaussian or any other Quantum Engines. This is carried out with the help of open babel using the following code. obabel initial.cml -O optimized.cml --minimize --steps 15000 --sd --log --ff MMFF94s. Here initial is the initial structure and optimized is the final output. –sd to use steepest descent algorithm –log will log all the proceding. Following all the force field that can be used:
C:\>obabel -L forcefields
GAFF    General Amber Force Field (GAFF).
Ghemical    Ghemical force field.
MMFF94    MMFF94 force field.
MMFF94s    MMFF94s force field.
UFF    Universal Force Field.

References

  • https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#forcefield-energy-and-minimization
  • https://avogadro.cc/