Category Archives: FAQ

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 […]