Tag Archives: Files

Where are the files for simulations?

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.

Which applications are available for visualizing downloaded files?

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 […]

Glycosylating Erythropoietin Using 1BUY.pdb

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 […]