pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules
- Mayk C. RamosMayk C. RamosInstituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, BrazilMore by Mayk C. Ramos
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- Patrick K. QuoikaPatrick K. QuoikaInstitute for General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020 Innsbruck, AustriaMore by Patrick K. Quoika
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- Vitor A. C. HortaVitor A. C. HortaInsight Centre for Data Analytics at Dublin City University, Dublin 9, IrelandMore by Vitor A. C. Horta
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- Douglas M. DiasDouglas M. DiasDepartment of Electronics and Telecommunications Engineering, State University of Rio de Janeiro, Rio de Janeiro 20550-900, BrazilMore by Douglas M. Dias
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- Elan G. CostaElan G. CostaDepartment of Electronics and Telecommunications Engineering, State University of Rio de Janeiro, Rio de Janeiro 20550-900, BrazilMore by Elan G. Costa
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- Jorge L. M. do AmaralJorge L. M. do AmaralDepartment of Electronics and Telecommunications Engineering, State University of Rio de Janeiro, Rio de Janeiro 20550-900, BrazilMore by Jorge L. M. do Amaral
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- Luigi M. RibeiroLuigi M. RibeiroDepartment of Electronics and Telecommunications Engineering, State University of Rio de Janeiro, Rio de Janeiro 20550-900, BrazilMore by Luigi M. Ribeiro
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- Klaus R. LiedlKlaus R. LiedlInstitute for General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020 Innsbruck, AustriaMore by Klaus R. Liedl
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- Bruno A. C. Horta*Bruno A. C. Horta*E-mail: [email protected]Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, BrazilMore by Bruno A. C. Horta
Abstract
The construction of a molecular topology file is a prerequisite for any classical molecular dynamics simulation. However, the generation of such a file may be very challenging at times, especially for large supramolecules. While many tools are available to provide topologies for large proteins and other biomolecules, the scientific community researching nonbiological systems is not equally well equipped. Here, we present a practical tool to generate topologies for arbitrary supramolecules: The pyPolyBuilder. In addition to linear polymer chains, it also provides the possibility to generate topologies of arbitrary, large, branched molecules, such as, e.g., dendrimers. Furthermore, it also generates reasonable starting structures for simulations of these molecules. pyPolyBuilder is a standalone command-line tool implemented in python. Therefore, it may be easily incorporated in persisting simulation pipelines on any operating systems and with different simulation engines. pyPolyBuilder is freely available on github: https://github.com/mssm-labmmol/pypolybuilder
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