Molecular Dynamics scripts for "Stoichiometric binding of Cyclophilin-A to the HIV-1 capsid modulates its mechanoelastic properties"

Scripts and example outputs for CypA decorated capsid AFM nanoindentation simuations in Rey, J.S., et. al. "Stoichiometric binding of Cyclophilin-A to the HIV-1 capsid modulates its mechanoelastic properties" Folders are organized as follows:0-build_cypA_capsid: Scripts necessary for building CypA decorated capsid models and mapping them to the SBCG representation1-afm_simulations: NAMD scripts for performind the AFM nanoindentation simulations using the slow and fast tip nanoindentation velocities. Output log files and the tcl and python scripts used to analyze the output are also included.Trajectories are not included due to large file size but can be acquired by contacting the authors.