Hi,
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!
Relly
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