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.
This FAQ entry refers to Step 3 of the Glyoprotein Builder, where glycosylation sites are chosen for a given glycan. Here, we have uploaded 1UBQ.pdb to use as an example. When you reach the “Attach Glycans” portion of the build, you will be presented with a list of potential glycosylation sites. They are divided into […]
Here is an image of a typical page where glycosylation sites are listed. The “Show All” buttons have been clicked so that all sites are shown, and not merely the most biologically relevant. These are potential glycosylation sites in PDB ID 1UBQ.pdb. Notice that the third location under “O-linking”, for residue 7, is not available […]
This question references the Options available when using the Glycoprotein Builder or any of the various interfaces to the Carbohydrate Builder (e.g., GAG Builder, Build-by-URL, Interactive Builder). In general, if you do not know for certain that you need to solvate or add counter ions, then you do not need to. These options are typically only […]