AMBER Archive (2008)
Subject: AMBER: [amber/glycam] dealing with fucose...
From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Hope every thing is working fine at your side.
Well, I am a new user of glycam and amber, just a couple of weeks old, and I am trying to do some studies with protein carbohydrate complex.
The complex that I have contains beta-d-galactose and alpha-l-fucose with the protein chain (The trisaccharide resides in the binding pocket of the protein and is not covalently attached to it).
With 2 galactoses one can rename them in the pdb file as 1GB and ZGB (since one galactose has linkage position 1, and the other one has linkage positions 2 and 3) but with fucose I am a bit confused because its not present in the standard glycam04 forcefield. I thought of building that residue with "biomolecule builder" (http://www.glycam.com/CCRC/biombuilder/biomb_index.jsp) but could not find a way to generate the prep & frcmod files for F1A (alpha-l-fucose with linkage position 1) residue that I need. I tried antechamber as well but there I do have some missing parameters.
What I am trying to do now is to find a way to generate the prep and frcmod files for this resiue in order to make it recognized in amber, so that I could rename this residue in pdb file and then load the whole pdb (with protein and carbohydrate) to generate top and crd files.
I appologize if my language is not that proper or clear. I hope that you did understand it. I request you to please let me know if I am on the right track or if there is some problem with my understanding of the subject matter.
I would really appreciate if you could respond.