Documentation for the releases of GLYCAM_06h and GLYCAM_06EPb 20120426 BLFoley Earlier documentation: For full GLYCAM_06 documentation, please see glycam.org/params Current changes overview: These releases make very few changes in the functioning of the force fields. However, there have been extensive formatting changes. It is important to note that these files will not work with previous releases of GLYCAM parameters. For this reason, all files were promoted to the same version (06h or 06EPb). Known limitations: The amino acid libraries for N- and O-linking glycans still have older, parm94/99-style atom type names. They will build molecules when used with the newer protein force fields, but the parameters used in the linking proteins will still be old. In version 06h-1, to be released soon, the amino acid linking files will be fully compatible with ff12SB. Summary of changes: * Atom type names were changed to fit a new uppercase-lowercase format. That is, CG was changed to Cg, HO was changed to Ho and so forth. The purpose of these changes is to ensure orthoganilty between GLYCAM parameters and those of other force fields. * The prep file databases for the main 06 and 06EP sets (not including lipids) were expanded and many corrections were made. The new entries should be more geometrically realistic and more stable when used in leap. These changes should allow more residues to be built than was possible before. Residues built before these changes are expected to have been built correctly, but their geometries might differ in minor ways. * A new van der Waals term was added for hydroxyl hydrogens. The term is very insubstantial in the course of a normal simulation. It was designed only to prevent catastrophic charge-charge collapses that can occur in certain circumstances. * Parameters appropriate to the protein force fields, to the extent they exist in our data set, were modified to be usable with ff12SB. Please see also "Known limitations", above. * The 06h leaprc was modified to call ion libraries consistent with ff12SB. * The 06EPb leaprc was modified to load TIP5P waters by default.