AMBER Archive (2003)

Subject: Re: Description of ATOM type in GLYCAM

From: FyD (fyd_at_u-picardie.fr)
Date: Tue Apr 29 2003 - 16:07:35 CDT

Dear Peng,

> I am trying to use GLYCAM in AMBER. I loaded the .prep and
> glycam_2000a.dat into xleap. But my system is mycolic acid which can
> not be recognized by GLYCAM force field correctly.
> Now, I want to assign the atom types manually in xleap.
> But I don't know how many atom types are there in
> GLYCAM force field, and the meaning of each type. I couldn't find such
> information anywhere.

- alpha sugars have 'AC' atom type for C1 atom,
- beta sugars have 'EC' atom type for C1 atom,
- endocyclic oxygen has the 'OS' atom type,
- exocyclic oxygen atoms implied in an hydroxyl group have the 'OH' atom type,
- exocyclic oxygen atoms implied in a bond with another sugar have the 'OG'
atom type,
- The other atom types (hydrogens: H1 & H2 atom types and carbons: CT) follow
the rules of the Cornell et al. FF.
(I think you do not need nitrogen atom types in mycolic acid...)

See also:
Glycam_93
- Woods, R. J.; Dwek, R.A.; Edge C.J. and B. Fraser-Reid, B. Molecular
Mechanical and Molecular Dynamical Simulations of Glycoproteins and
Oligosaccharides. 1. GLYCAM_93 Parameter Development. J. Phys. Chem. 1995, 99,
3832-3846.
Newer Glycam FF:
- Pathiaseril, A. and Woods, R. J. Relative Energies of Binding for Antibody-
Carbohydrate-Antigen Complexes Computed from free-Energy Simulations. J. Am.
Chem. Soc. 2000, 122, 331-338.

regards, Francois