References

PsiRESP is built on published scientific work. Please cite the relevant references when using PsiRESP in published work, specifically the citation in Pre-configured classes.

PsiRESP uses the Connolly algorithm to generate molecular surfaces [Con83].

Citations with Duecredit

Some citations can be automatically generated with duecredit. This is installed with the conda environment files in devtools/, or can be otherwise installed with:

pip install duecredit

Generate a bibliography with:

cd /path/to/yourmodule
python -m duecredit yourscript.py

Do it in the BibTeX format, using:

duecredit summary --format=bibtex

Bibliography

ABS20: Asem Alenaizan, Lori A. Burns, and C. David Sherrill. Python implementation of the restrained electrostatic potential charge model. International Journal of Quantum Chemistry, 120(2):e26035, 2020. 00000 _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.26035. URL: http://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26035 (visited on 2020-05-01), doi:10.1002/qua.26035.
BCCK93: Christopher I. Bayly, Piotr Cieplak, Wendy Cornell, and Peter A. Kollman. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. The Journal of Physical Chemistry, 97(40):10269–10280, October 1993. 04975. URL: http://pubs.acs.org/doi/abs/10.1021/j100142a004 (visited on 2019-08-06), doi:10.1021/j100142a004.
CCBK95: Piotr Cieplak, Wendy D. Cornell, Christopher Bayly, and Peter A. Kollman. Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins. Journal of Computational Chemistry, 16(11):1357–1377, November 1995. 00876. URL: http://doi.wiley.com/10.1002/jcc.540161106 (visited on 2019-08-06), doi:10.1002/jcc.540161106.
Con83: M. L. Connolly. Analytical molecular surface calculation. Journal of Applied Crystallography, 16(5):548–558, 1983. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1107/S0021889883010985. URL: http://onlinelibrary.wiley.com/doi/abs/10.1107/S0021889883010985 (visited on 2021-04-05), doi:https://doi.org/10.1107/S0021889883010985.
CCBK93: Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, and Peter A. Kollman. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. Journal of the American Chemical Society, 115(21):9620–9631, October 1993. 01110. URL: http://pubs.acs.org/doi/abs/10.1021/ja00074a030 (visited on 2019-08-06), doi:10.1021/ja00074a030.
DCL+07: F.-Y. Dupradeau, C. Cezard, R. Lelong, E. Stanislawiak, J. Pecher, J. C. Delepine, and P. Cieplak. R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries. Nucleic Acids Research, 36(Database):D360–D367, December 2007. 00081. URL: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkm887 (visited on 2019-08-06), doi:10.1093/nar/gkm887.
DPZ+10: François-Yves Dupradeau, Adrien Pigache, Thomas Zaffran, Corentin Savineau, Rodolphe Lelong, Nicolas Grivel, Dimitri Lelong, Wilfried Rosanski, and Piotr Cieplak. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. Physical Chemistry Chemical Physics, 12(28):7821, 2010. 00595. URL: http://xlink.rsc.org/?DOI=c0cp00111b (visited on 2019-08-06), doi:10.1039/c0cp00111b.
Lan: Gregory Landrum. RDKit: Open-source cheminformatics. https://doi.org/10.5281/zenodo.4107869. URL: rdkit.org.
MZB+11: Alpeshkumar K. Malde, Le Zuo, Matthew Breeze, Martin Stroet, David Poger, Pramod C. Nair, Chris Oostenbrink, and Alan E. Mark. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12):4026–4037, December 2011. 00000. URL: https://pubs.acs.org/doi/10.1021/ct200196m (visited on 2019-05-29), doi:10.1021/ct200196m.
SNJ+20: Michael Schauperl, Paul S. Nerenberg, Hyesu Jang, Lee-Ping Wang, Christopher I. Bayly, David L. Mobley, and Michael K. Gilson. Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2). Communications Chemistry, 3(1):1–11, April 2020. 00000 Number: 1 Publisher: Nature Publishing Group. URL: https://www.nature.com/articles/s42004-020-0291-4 (visited on 2020-05-13), doi:10.1038/s42004-020-0291-4.
SK84: U. Chandra Singh and Peter A. Kollman. An approach to computing electrostatic charges for molecules. Journal of Computational Chemistry, 5(2):129–145, 1984. 00000 _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.540050204. URL: http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540050204 (visited on 2020-05-11), doi:10.1002/jcc.540050204.
TSP+12: Justin M. Turney, Andrew C. Simmonett, Robert M. Parrish, Edward G. Hohenstein, Francesco A. Evangelista, Justin T. Fermann, Benjamin J. Mintz, Lori A. Burns, Jeremiah J. Wilke, Micah L. Abrams, Nicholas J. Russ, Matthew L. Leininger, Curtis L. Janssen, Edward T. Seidl, Wesley D. Allen, Henry F. Schaefer, Rollin A. King, Edward F. Valeev, C. David Sherrill, and T. Daniel Crawford. Psi4: an open-source ab initio electronic structure program. WIREs Computational Molecular Science, 2(4):556–565, 2012. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/wcms.93. URL: http://onlinelibrary.wiley.com/doi/abs/10.1002/wcms.93 (visited on 2021-04-05), doi:https://doi.org/10.1002/wcms.93.