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bioRxiv · 10.1101/2025.01.07.631713

PyPE_RESP: A tool to facilitate and standardize derivation of RESP charges

Lapsien, M.·Bonus, M.·Gahan, L.·Raguin, A.·Gohlke, H.
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Abstract

We introduce PyPE_RESP, a tool to facilitate and standardize partial atomic charge derivation using the RESP approach. PyPE_RESP builds upon the open-source Python package RDKit for chemoinformatics and the AMBER suite for molecular simulations. PyPE_RESP provides an easy setup of multi-conformer and multi-molecule Restrained Electrostatic Potential (RESP) fitting while allowing a comprehensive definition of charge constraint groups through multiple methods. As a command line tool, PyPE_RESP can be integrated into batch processes. The software enables the derivation of partial atomic charges for additive and polarizable force fields. It outputs constraint group and non-constraint group charges to give an immediate overview of the fit result. PyPE_RESP will be distributed with AmberTools and compatible with most computing platforms. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/631713v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@7fc123org.highwire.dtl.DTLVardef@16102f0org.highwire.dtl.DTLVardef@8044dorg.highwire.dtl.DTLVardef@5277f8_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Lapsien, M., Bonus, M., Gahan, L., Raguin, A., Gohlke, H.. 2025-01-08. PyPE_RESP: A tool to facilitate and standardize derivation of RESP charges. https://doi.org/10.1101/2025.01.07.631713

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