Molecular dynamics and Rosetta scripts for "MxB N-Terminus Adopts a Stable α-Helix to Engage the HIV-1 Capsid Trimer Interface"
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Scripts, inputs and example outputs for the simulations described on MxB N-Terminus Adopts a Stable α-Helix to Engage the HIV-1 Capsid Trimer Interface Files herein are organized in three directories: 1-CA_MDFF : Input files, scripts and output structures from Molecular Dynamics Flexible Fitting (MDFF0) simulations of the CA trimer of dimers into the STA density. Based on representative structures of CA-MxB simulations from Smaga et.al. Structure 2019 (https://doi.org/10.1016/j.str.2019.04.0150) 2-CA_MxB_RosettCM : Input files, scripts and output structures from RosettaCM modeling of MxB into the CA trimer of dimers structure based on the STA CA-MxB density and an AlphaFold-derived MxB template. 3-MD : Input files, scripts and example outputs for the Molecular Dynamics (MD) simulations of CA-MxB complex as well as analysis scripts and outputs. Necessary software:NAMD >= 3.0 (to perform MD simulations)VMD >= 1.9 (to execute the Tcl analysis scripts and to prepare the CA-MxB systems for simulation)Rosetta installation with Rosetta Scripts >=2021.16 (To generate structure ensembles of MxB guided by the STA density)Amber and AmberTools >=22 (To perform MMGBSA analysis of the MD trajectories) If you have any questions, don't hesitate to contact Juan S. Rey (jsreyl@udel.edu) or Juan R. Perilla (jperilla@udel.edu).
