There are two sets of parameters: one without extra points (aka electron lone pairs), and one with extra points. These files include a leaprc (leaprc.Glycam), carbohydrate prep files with ensemble average charge set (Glycam04.prep), and the parameter file (Glycam04.dat). The files associated with extra points have "EP" in the file name.
At all times, our website will contain the most recent version of the Glycam parameter file set. Over time, we will be adding additional prep residues and modify the other files as the need arises.
Please feel free to comment about this parameter set and make suggestions about how it may be improved in the future. Also, please comment on any bugs that you might find when using these files. As pointed out before, please read the AMBER8 manual before implementing Glycam04.
Notes: This force field my be employed independently for simulating carbohydrtes or may be used in conjunction with Parm94 without introducing any conflict. Correct rotational behavior for O-C-C-O fragments requires SCEE=SCNB=1.0. This is in contrast to "standard" AMBER, in which it is normal to set SCEE=1.2 and SCNB=2.0. Unless you are attempting to generate rotamerpopulations, it is OK to use the "standard" values. Using non-standard values (SCEE=SCNB=1.0) may be unacceptable when a protein is also present. To obtain the current version of this force field and/or carbohydrate prep files go to the website http://www.glycam.ccrc.uga.edu.
GLYCAM contributors include: Karl N. Kirschner, Sarah Tschampel, Robert Woods