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 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 […]

Which protein force fields are compatible with GLYCAM?

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 […]

How can I use GLYCAM files in the oldff directory?

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 […]

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 […]