{"title":"PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing.","authors":"Jian Huang, Chenchen Wu, Xiner Yang, Zaixing Yang, Shengtang Liu, Gang Yu","doi":"10.1021/acs.jcim.4c01639","DOIUrl":null,"url":null,"abstract":"<p><p>PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its tremendous advantages have been impeded by the longstanding lack of a robust open-source graphical user interface (GUI) that integrates parameter settings with the visualization of molecular and geometric constraints. To address this limitation, we have developed PACKMOL-GUI, a VMD plugin that leverages the dynamic extensibility of the Tcl/Tk toolkit. This GUI enables the configuration of all PACKMOL parameters through an intuitive user panel, while also facilitating the visualization of molecular structures and geometric constraints, including cubes, boxes, and spheres, among others via the VMD software. The seamless interaction between the VMD and PACKMOL provides an intuitive and efficient all-in-one platform for the packing of complex molecular systems.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"778-784"},"PeriodicalIF":5.3000,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776922/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.4c01639","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/11 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0
Abstract
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its tremendous advantages have been impeded by the longstanding lack of a robust open-source graphical user interface (GUI) that integrates parameter settings with the visualization of molecular and geometric constraints. To address this limitation, we have developed PACKMOL-GUI, a VMD plugin that leverages the dynamic extensibility of the Tcl/Tk toolkit. This GUI enables the configuration of all PACKMOL parameters through an intuitive user panel, while also facilitating the visualization of molecular structures and geometric constraints, including cubes, boxes, and spheres, among others via the VMD software. The seamless interaction between the VMD and PACKMOL provides an intuitive and efficient all-in-one platform for the packing of complex molecular systems.
期刊介绍：
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.
Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field.
As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
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