This manual describes the procedure how to build molecular description files (.mmol) for MDynaMix implementing GAFF force field. According to the GAFF force field definition, the partial charges for atoms should be determined by the ab-initio Hartree-Fock computations for the optimized molecular geometry, with the 6-31 (d) basis set and restricted electrostatic potential fitting (RESP) method (J. Phys. Chem., 1993, 97 (40), pp 10269–10280).
Avogadro (free open source cross-platform molecular editor)
Antechamber package of Amber Tools (can be downloaded and installed without purchasing Amber)
Makemol utility of MDynaMix v. 5.2.7 or higher
1. Generation of molecular structure (Avogadro)
Start Avogadro. Build the molecule using tools of Avogadro. Optimize geometry (from "Extension" menu). Save the molecule as "Gaussian Cartesian Input (*.gau)". Assume further name of the molecule be sample.gau.
2. Geometry optimization and computation of ESP charges (Gaussian)
Run Gaussian to finally optimize geometry and compute partial charges using the standard electrostatic potential fitting. Gaussian command line for this run (which substitute the command line in Avogadro output) can be:
# Opt HF/6-31G(d) Pop=MK IOp(6/33=2,6/41=10,6/42=17)
Comments:
"IOp" parameter 6/33=2 instructs to write the electrostatic potential information to the output file for further analysis by Antechamber. Two other parameters can be used to regulate the grid for the electrostatic potential fitting, the number of surfaces around the atoms (6/41=10) and the density of test points on these surfaces (6/42=17).
Assume that the output Gaussian file is sample.gout
3. Computation of RESP charges and assigning of GAFF atom types (antechamber)
Run antechamber to assign GAFF atom types and to finally compute partial charges using RESP algorithm:
antechamber -fi gout -i sample.gout -fo mol2 -o sample.mol2 -c resp
4. Building of molecular description file for MDynaMix (makemol)
Use makemol utility of MDynaMix to convert .mol2 file to .mmol format:
makemol sample.mol2 gaff.ff
Here gaff.ff is GAFF parameter file from the MDynaMix makemol directory, which should be copied into the working directory. The generated sample.mmol file can be used directly in MD simulations by MDynaMix.