Where can I find the VINA-Carb program?
The easiest place to find it is here: http://glycam.org/docs/othertoolsservice/downloads/downloads-software/
Tag Archives: Force Field
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 are CHI Energy Functions?
The CHI (Carbohydrate Intrinsic) energy functions score oligosaccharide structures based on glycosidic linkage conformations. Glycosidic torsion angles that deviate from the calculated global energy minima are penalized according to the energy curves. The functions were developed by fitting Gaussian equations to the torsional energy profiles of tetrahydropyran-based disaccharide models, which were obtained using quantum mechanical […]
What do the file versions mean in the GLYCAM force fields?
Click here to learn more about file versioning for the GLYCAM parameter sets.
Why are there so many different files for GLYCAM06?
We have occasionally needed to make changes to the GLYCAM06 parameter files. Whenever we do, we give the file a new version number. Click here to learn more about file versioning for the GLYCAM parameter sets.
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 […]