In the project of investigation of substituent effect on properties of aromatic halogen atoms the Electrostatic Tools programs were used as a tool to fit a series of electrostatic models. Two types of models were built: multipole-based (ME) one and extra-point-based one (EP).
In this project the Electrostatic Tools programs were used as a tool to fit a series of electrostatic models. Two types of models were built: multipole-based (ME) one and extra-point-based one (EP).
You can reproduce the final models for the structure set. For this purpose you will need to download the set (tar.bz2 - 43Mb or tar.xz - 32Mb) containing files with structures, reference MEP grids, multipole placement rules and a file with molecular descriptors. Untar it and change to "set" directory. You will find several directories and files:
- structures is a directory, containing "mol{1..730}.mol2" and "mol{1..730}.at.mol" files. The first ones are molecular structures of the set, the second group contains tha same structures but with "halogen" hydrogens and fluorines (see the publication for the details) changed to At so we can distinguish them from other H and F.
- png is a directory containing structural formulae of the molecules in PNG format.
- grids is a directory containing reference MEP grids for the set in ESP format.
- ME and EP are empty directories where we are going to save fit results.
- mq_.rules is a multipole placement rulefile for fitter programs.
- descriptors.txt is a text file containing tab-separated columns with Free-Wilson and Hansch descriptors used in QSPR study (see the publication for more info)
- get_params_me.py and get_params_ep.py are scripts to extract fitted data.
To fit ME and EP models issue the following command from "set" directory (assuming your shell is bash):
for i in mol{1..730}
do
mult_fitter -I structures/${i}.at.mol2 -G grids/${i}.6-31G_SBKJC.rhf.4c5l.esp -O ME/${i}.me.mmol -L ME/${i}.me.log -p mq_.rules
ep_fitter -I structures/${i}.at.mol2 -G grids/${i}.6-31G_SBKJC.rhf.4c5l.esp -O EP/${i}.ep.mmol -L EP/${i}.ep.log -p mq_.rules -x 1.33 -M"[Cl,Br,I,At]"
done
The execution will take some time (about 3 minutes). Normally you should not see any console output. To collect the data issue the following commands:
echo "me_rmsd" > ME.rmsd.txt
echo "ep_rmsd" > EP.rmsd.txt
for i in mol{1..730}
do
grep ME/${i}.me.mmol -e "RMSD" | awk '{print $2}' >> ME.rmsd.txt
grep EP/${i}.ep.mmol -e "RMSD" | awk '{print $2}' >> EP.rmsd.txt
done
python3 get_params_me.py > params_me.txt
python3 get_params_ep.py > params_ep.txt
Now you can use the fitted data for further analysis in any kind of statistical program, for example GNU R.