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Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories

Authors

  • Panagiotis I. Koukos,

    1. Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, Greece
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  • Nicholas M. Glykos

    Corresponding author
    • Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, Greece
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Fax: (+30) 25510 30620 E-mail: glykos@mbg.duth.gr

Abstract

We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross-platform, Perl/Tk-based front-end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user-friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root-mean-square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free-open source software available immediately for download. © 2013 Wiley Periodicals, Inc.

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