Files for running simulations can only be downloaded if you choose to download all files. You can choose between a zip or tgz (tar + gzipped) archive. The archive contains a number of files, including the parameter-topology (prmtop, parm7) and input-coordinate (inpcrd, rst7) files you need for AMBER molecular dynamics simulations.
Once the build of the carbohydrate molecule is complete, it can be downloaded and visualized. Visual molecular dynamics (VMD) is one program that can be used to visualize these files. VMD displays molecular surfaces with fast surface calculation and display. The high performance algorithms allow even complex surfaces to be displayed. To download this program click […]
Overview In this exercise, we will: Download a PDB structure of a mutated protein. In its native state, the protein is glycosylated, and it does not perform its functions properly without at least some of the glycosylation. Use the text editor and the utilities at GLYCAM-Web to change the mutated residues back to the natural […]
Click here to learn more about file versioning for the GLYCAM parameter sets.
We have occasionally needed to make changes to the GLYCAM06 parameter files. Whenever we do, we give the file a new version number. Click here to learn more about file versioning for the GLYCAM parameter sets.