[gmx-users] virtual atoms: hydrogens on sugars

Relly Brandman rbrandman at hotmail.com
Mon Mar 16 21:14:19 CET 2009

I'm trying to create virtual atoms for the hydrogens in a glycosylated protein, specifically the hydrogens on the sugar. I have three types of hydrogens bound to carbon: CH on ring carbon, CH2 on branched carbon,  CH3 methyl group. I also have OH and NH hydrogens.
Three questions:
1. Should all of these be 4fd type hydrogens because they are all ~sp3 hybridized geometry around the carbon (puckered ring, branched, methyl)?
2. I understand that I'll have to add a line like the following for each of my virtual atoms.  Can somebody please clarify what function 1 is, and what the a,b and d parameters are? 
[ virtual sites4 ]
; Site from funct a b d
5 1 2 3 4 1 0.33333 0.33333 -0.105
3. What is the best way to handle the OH and NH hydrogens?
Thank you for any advice!
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