TY - GEN

T1 - Charge group partitioning in biomolecular simulation

AU - Canzar, Stefan

AU - El-Kebir, Mohammed

AU - Pool, René

AU - Elbassioni, Khaled

AU - Malde, Alpesh K.

AU - Mark, Alan E.

AU - Geerke, Daan P.

AU - Stougie, Leen

AU - Klau, Gunnar W.

PY - 2012

Y1 - 2012

N2 - Molecular simulation techniques are increasingly being used to study biomolecular systems at an atomic level. Such simulations rely on empirical force fields to represent the intermolecular interactions. There are many different force fields available|each based on a different set of assumptions and thus requiring different parametrization procedures. Recently, efforts have been made to fully automate the assignment of force-field parameters, including atomic partial charges, for novel molecules. In this work, we focus on a problem arising in the automated parametrization of molecules for use in combination with the gromos family of force fields: namely, the assignment of atoms to charge groups such that for every charge group the sum of the partial charges is ideally equal to its formal charge. In addition, charge groups are required to have size at most κ. We show NP-hardness and give an exact algorithm capable of solving practical problem instances to provable optimality in a fraction of a second.

AB - Molecular simulation techniques are increasingly being used to study biomolecular systems at an atomic level. Such simulations rely on empirical force fields to represent the intermolecular interactions. There are many different force fields available|each based on a different set of assumptions and thus requiring different parametrization procedures. Recently, efforts have been made to fully automate the assignment of force-field parameters, including atomic partial charges, for novel molecules. In this work, we focus on a problem arising in the automated parametrization of molecules for use in combination with the gromos family of force fields: namely, the assignment of atoms to charge groups such that for every charge group the sum of the partial charges is ideally equal to its formal charge. In addition, charge groups are required to have size at most κ. We show NP-hardness and give an exact algorithm capable of solving practical problem instances to provable optimality in a fraction of a second.

UR - http://www.scopus.com/inward/record.url?scp=84860811847&partnerID=8YFLogxK

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U2 - 10.1007/978-3-642-29627-7_3

DO - 10.1007/978-3-642-29627-7_3

M3 - Conference contribution

AN - SCOPUS:84860811847

SN - 9783642296260

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 29

EP - 43

BT - Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings

T2 - 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012

Y2 - 21 April 2012 through 24 April 2012

ER -