First, try using a file that has already been tested, such as this file generated from the GLYCAM Web-Builder OR PDB ID: 3SGJ. If those files work properly, but your original does not, check the file to ensure the pdb is in the proper format (compared to the provided files). For example, a .pdbqt file […]
The easiest place to find it is here: http://legacy.glycam.org/docs/othertoolsservice/downloads/downloads-software/
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 […]
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 […]
BFMP is a method for naming conformations of six-member rings. It is similar to the IUPAC method (that, e.g., uses 1C4 for one of the chair conformations), but it is more flexible. It is able to unambiguously name symmetrical and asymmetrical shapes. It can also give information regarding the degree to which a shape deviates […]
This question refers to all variants of the Carbohydrate Builder, including those that interface to the Glycoprotein Builder. For most monosaccharides, the aglycon will make very little difference to the molecular structure. Even for ketoses (see image below), the steric interactions primarily involve exocyclic rotations around highly rotatable bonds. So, in most cases the choice […]
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 […]
This is actually two different questions. Both will be addressed here. Question 1: In a simulation, which protein force fields behave well with GLYCAM? The GLYCAM force fields are designed to be independent of other biomolecular force fields, and, therefore, to work at least reasonably well with any of them. The philosophy is that if […]
This question refers to the leaprc files stored in $AMBERHOME/dat/leap/cmd/oldff in distributions of AmberTools. Before answering the question, it is important to know that files in the oldff directory have been placed there because they are no longer recommended. It isn’t necessarily that those old force fields are terrible; it’s just that the newer ones […]