AMBER Archive (2004)

Subject: Re: AMBER: Residue Charges

From: Rhonda Torres (torres_at_scripps.edu)
Date: Tue Mar 23 2004 - 11:51:55 CST

On Tue, 23 Mar 2004 opitz_at_che.udel.edu wrote:

> 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?

The residue will have an integer charge, be it positive, negative or
neutral. The structure, once put together, should have an integer charge
as well.

> 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

It is not clear what you are referring to here. We would need more
information to effectively answer this question.

Rhonda

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