Created by Hugo Azurmendi; January 2024 Email: hugo.azurmendi@fda.hhs.gov Link to this folder: https://github.com/FDA/MD-of-Glycans
This folder contains essential files to reproduce Molecular Dynamics (MD) results of the 2024 PNAS article: "The structure of a C. neoformans polysaccharide motif recognized by protective antibodies: A combined NMR and MD study".
IMPORTANT: For easy exploration, we recommend downloading the whole directory by clicking the green button "<> Code" and selecting 'Download zip'. This will generate this folder with all content in your default Download folder (total size is ~37 MB). You may then move the folder to a convenient location of your choice.
The MD studies were done using the AMBER20 software package and run on Linux, Centos 7, GPUs. Basic familiarity with AMBER, BASH and Linux is required to use the provided scripts.
Starting coordinates and parameter files were created using the 'tleap' AMBER program. Within the 'build-' folders are the input files to generate the starting coordinates and parameter files. To execute, 'cd' to one of the 'build' folders and in terminal enter (with AMBER properly installed; '[]' is optional to generate an output log file): tleap -f leapIn.txt [> leapOut*.log]
We implemented the Hydrogen Mass Repartition (HMR) method to speed up MD simulations. For this, the normal parameter file generated with 'tleap' (.prmtop) must be modified using the AMBER program 'parmed'. In addition, modified saccharides may require adjustment of charges to make them neutral. This was necessary for O-acetylated mannoses. The parmed input scripts provided fix this as well. On terminal do: parmed -i parmedIn-.txt [> parmedOut-*.log]
The commands above were executed to include results in the 'build-' folders, with the output messages saved as '.log' text files. You may rerun the scripts, but keep in mind that 'parmed' doesn't overwrite parameter files by default. Once the above steps are done the simulation can be started using the provided adaptable script 'mdrun-full.txt'. Read the comments in the script for details.
Two partial MD trajectories, discussed in the paper, are included as compressed zip files in the root folder, one for gxm10-Ac3 (2000 frames -> 2 mcs duration), and one for GXM12RU (last 500 frames, 500 ns).