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 […]

Which aglycon (aglycone) should I use?

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 […]

Should I solvate and/or add counter ions?

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 […]

What molecules can I build using GLYCAM?

Answer in progress…. Please pardon any mess while this page is being built.  In the meantime, perhaps the information will be of use.  If you have questions, please contact us. The tables below list the current capabilities of the GLYCAM-Web parameter sets. Note: these capabilities might differ slightly from those of the point-and-click builder.  They […]