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 […]
Determining the ring conformation of Iduronic acid from a PDB file using BFMP. If needed, please click here for instructions on downloading and installing the BFMP program. The program requires two input files: a text file in PDB format and a configuration file. Click here to download BFMP-Tutorial2.tar.gz, the input and output files for this tutorial Using vi or […]
Determining the ring conformation of A-L-Idopyranose during the course of a 10ns MD simulation using BFMP. If needed, please click here for instructions on downloading and installing the BFMP program. The program requires three input files: an AMBER format topology file, AMBER format trajectory file and a configuration file. Click here to download BFMP-Tutorial1.tar.gz, the Input AMBER format files and output […]
On this site, these terms apply to software, data and other materials that are available for download. An associated publication either announced the availability of a download or necessitated a download. For example, it might be a publication describing a program available for download or a publication explaining a class of force fields for which we provide […]