AMBER Archive (2006)

Subject: Fwd: AMBER: LEaP error : unbalanced charge

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Fri Jun 16 2006 - 11:34:42 CDT


Dear Thomas

Thank you for your suggestions but I don't know how to check charges for the
deprotonated tyrosine. Please give me more details.

Best regard,

 Jitrayut Jitonnom, Ph.D.
Dept. of Chemistry,
Computational Simulation,
and Modeling Laboratory (CSML),
Chiang Mai University, Thailand.
Email: jitrayut.018_at_gmail.com <shafinaz_at_bri.nrc.ca>
Tel: +66(0)6613-4218

---------- Forwarded message ----------
From: Thomas Steinbrecher <steinbrt_at_scripps.edu>
Date: 16 .. 2006, 21:59 .
Subject: Re: AMBER: LEaP error : unbalanced charge
To: amber_at_scripps.edu

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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