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.
The script functions by: Identify residues that contain a 6-membered ring AND have atom names C1, C2, C3, C4, C5, and O5 Determine the geometric center of the ring for residues from Step 1 Identify the geometric center of the connecting residue by 1) determining the oxygen that is connected to C1 and is NOT […]
The diameter of the sphere in the 3D-SNFG representation is exactly 4 Å, and the other shapes are scaled around the sphere. This size for the sphere was chosen based on the cross-section of a monosaccharide ring, which is approximately 4 Å in one direction and 6 Å in another. Although we tested shapes at […]
This error message is harmless. The provided vmdrc files apply specific representations to the first molecule that is loaded into the program (i.e. proteins displayed in NewCartoon and hetero atoms as licorice). If a molecule is not loaded upon initializing VMD, either by double-clicking the PDB file or through the command line (i.e. ‘vmd 3SGJ.pdb’), […]
Yes, the structures that were used to generate each of the Glycan images in the Gallery may be downloaded by clicking on the name of the respective structure. Additionally, each PDB referenced in the gallery is available directly from the RCSB database.
Symbols within the SNFG nomenclature refer to either the D or L form of the monosaccharide based upon what is most common in nature. The 3D-SNFG code does NOT differentiate between L and D residues. For example, the red triangle within the SNFG refers to an L-Fucose; however, both L and D Fucose are represented […]
Sugar modifications are not currently displayed in 3D-SNFG, although the base shape is shown. The SNFG icons are an effective method for communicating the modifications on residues. For example, the following is a heparan sulfate fragment built with the GLYCAM Webtool: Using the 3D-SNFG icons conveys both the residue name and sulfation position. Representing the […]
If multiple PDB files are loaded within VMD, the representation will only be drawn on the ‘top’ molecule. In order to apply the representations to any of the other files, change the ‘top’ molecule by double clicking the blank space in the T column in the Main Window. Alternatively, change the top molecule via the […]
The easiest solution is to change the residue name in the PDB file to one that is already recognized by the script. Use any text editor to open the PDB file and modify the fourth column. Find and replace is useful, or use a substitution method via the command line (i.e. ‘sed‘ or ‘vi‘). If […]
Check the PDB file to ensure that the ring atoms are properly named. For most monosaccharides, they should be C1, C2, C3, C4, C5. If the residue is a sialic acid, the ring atoms should be C2, C3, C4, C5, C6, and O6. Example error message from command line: ERROR) vecsub: two vectors don’t have […]