Date of Award

May 2019

Degree Type


Degree Name

Master of Science (MS)


Biomedical and Chemical Engineering


Shikha Nangia

Subject Categories



Peptidoglycan (PG), also known as murein, is an essential component in both Gram-positive and Gram-negative bacteria. However, even if the chemical structure has been well-known for long, the great tertiary structure remains not clear due to its variability and complicated cross-link mechanism. And it inevitably raises the huge challenge for computational simulations. Against the background, here we present a method for building a solvated peptidoglycan system at coarse-grained level as required. The method is named PEPpy, which represents a Peptidoglycan python code. It reads in the user’s parameters in sequence and automatically generates a topological file and a structure file in the meantime. With these files generated, molecular dynamics simulations and a series of analyses can be easily performed afterwards.


Open Access

Available for download on Saturday, June 05, 2021

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Engineering Commons