AMBER Archive (2006)

Subject: Re: AMBER: LEaP error : unbalanced charge

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Fri Jun 16 2006 - 09:59:50 CDT

Dear Jitrayut,

> I am studying the protonation state of heptapeptide binding with enzyme. In
> this work, I also used RESP charge model to calculate deprotonate tyrosine.
> But I found 1 error about total charge (-17.4815 ,do not add Na+ yet) when I
> do LEaP. So, my question is "Can I balance this charge to zero ?", if
> not, it means that this charge can be ignored right ? Or maybe someone can

This sounds like something that should not be ignored. All the different
molecules in your system should have integer charges. Check where the
.48 charge is located and take a close look if the partial charges there
are reasonable. My guess would be that something in your resp calculation
went wrong. Do the charges for the deprotonated tyrosine differ much from
those of the regular tyrosine residue?

Thomas
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