Molecular dynamics scripts for "Structural basis for HIV-1 capsid adaption to a deficiency in IP6 packaging"

Code and input files for the molecular dynamics simulations performed in Zhu, Yanan, et. al. "Structural basis for HIV-1 capsid adaption to a deficiency in IP6 packaging" Nature Communications (2025) https://doi.org/10.1038/s41467-025-63363-9 The files are organized in two fodlers: - MD_simulations: contains input structures, parameters and input files to run all MD simulations decribed in the manuscript of the CA trimer of dimers with WT, KAKA and KAKA/G225R sequences- analysis_scripts: contains bash and tcl scripts used for analyzing the MD trajectories and calculating RMSD, RMSF and CA C-terminal region occupancies Necessary software:NAMD >=3.0 (to run MD simulations)VMD 1.9.4a57 (to execute the analysis Tcl scripts) If you have any questions, don't hesitate to contact [email protected] or [email protected]