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Broadening access to small-molecule parameterization with the force field toolkit.

Authors :
Zeng, Yunlin
Pavlova, Anna
Nelson, Philip M.
Glick, Zachary L.
Yang, Lan
Pang, Yui Tik
Spivak, Mariano
Licari, Giuseppe
Tajkhorshid, Emad
Sherrill, C. David
Gumbart, James C.
Source :
Journal of Chemical Physics. 6/28/2024, Vol. 160 Issue 24, p1-12. 12p.
Publication Year :
2024

Abstract

Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
00219606
Volume :
160
Issue :
24
Database :
Academic Search Index
Journal :
Journal of Chemical Physics
Publication Type :
Academic Journal
Accession number :
178147220
Full Text :
https://doi.org/10.1063/5.0196848