How to get CM5 charges for Condensed Phase Simulations?

CM5 charges

Some background 👍

In 2014-2015, Jorgensen group has published a series of papers exploring the usability of CM5 charges for condensed phase simulations. CM5 charge model is a very simple, elegant and easy to implement charge model from Marinech and co-workers [2]. Some of the positive and negative aspects of CM5 charges in comparison with CM1A charges are explained in the references below[1,3,4].

In brief, here are some take-home messages

• CM5 charges are based on DFT/MP2 calculation and use Hirshfeld population analysis.

  • Very Slow for Organic Drug-like molecules
  • Need QM software (CM5 charges are only available in Gaussian, this blog post alleviates this problem 👍)
  • Is parameterized with bigger data set compared to CM1A charges

But how to get these CM5 charges if you don't have a Gaussian license?

Answer is ORCA to know more about ORCA and its capabilities check out this website by ORCA authors

https://sites.google.com/site/orcainputlibrary/orbital-and-density-analysis

Step 1: QM calculation with ORCA

For any molecule of your choice run the orca calculation with the following input file, with xyz coordinates of the molecule saved in a file called inp_orca.xyz

!RKS RIJCOSX M062X cc-pVDZ PMODEL
% output
        Print[P_hirshfeld] 1
 end
*xyzfile 0 1 inp_orca.xyz

run this input file using the following command $ORCA_DIR/orca file_name.inp > qm_orca.log

Step 2: Get CM5 charges from ORCA log file.

Next step is to convert these Hirshfeld charges to CM5 charges. To do this I have written a python script https://github.com/leelasd/ligpargen/blob/master/Orca2CM5charges.py

that takes the orca log file as input and prints CM5 charges.

python Orca2CM5charges.py -o qm_orca.log

This creates a CSV file called CM5_charges.csv which contains XYZ coordinates, CM5 charges from QM calculation, CM5 charges averaged according to the different atom types (with and without scale factor of 1.20 to account for solvent polarization).
you can use these charges to do MD/MC simulations in combination with OPLS-AA force fields from LigParGen server.

Please cite following references if you use the code

1. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
   Leela S. Dodda Israel Cabeza de Vaca Julian Tirado-Rives William L. Jorgensen Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W331–W336

2. Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases Marenich, A. V.; Jerome, S. V.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2012, 8, 527– 541

3. Evaluation of CM5 Charges for Condensed-Phase Modeling Jonah Z. Vilseck, Julian Tirado-Rives, and William L. Jorgensen J. Chem. Theory Comput., 2014, 10 (7), pp 2802–2812

4. Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling Leela S. Dodda, Jonah Z. Vilseck, Kara J. Cutrona, and William L.Jorgensen J. Chem. Theory Comput., 2015, 11 (9), pp 4273–428