Marco Lapsien, Michele Bonus, Lianne Gahan, Adélaïde Raguin, Holger Gohlke
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PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges.
We introduce PyPE_RESP, a tool to facilitate and standardize partial atomic charge derivation using the Restrained Electrostatic Potential (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 multiconformer and multimolecule 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 nonconstraint group charges to give an immediate overview of the fit result. PyPE_RESP will be distributed with AmberTools and compatible with most computing platforms.
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The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery.
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