AMBER Archive (2004)

Subject: AMBER: Residue Charges

From: opitz_at_che.udel.edu
Date: Tue Mar 23 2004 - 09:17:38 CST

('binary' encoding is not supported, stored as-is) Dear Amber Community,

I have a quick question concerning the charge distribution on residues.
Is the residue by itself supposed to be neutral (or negative or positive,
whichever be the case) by itself? Or is the structure once put together
supposed to be neutral?
If the residue itself is neutral, doesn't that introduce charges that are
uncharacteristically too high or too low compared to the real molecule?
And if that is the case, why has that been accepted as correct, I mean
what is the justification for it?

Thanks,

Armin

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