AMBER Archive (2007)

Subject: Re: AMBER: ADDIONS do not neutralize to ZERO

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jan 22 2007 - 19:58:11 CST


>> addions2 ang Cl- 0
> ERROR: The unperturbed charge of the unit: 0.970410 is not integral.
> WARNING: The unperturbed charge of the unit: 0.970410 is not zero.

> I defined in my command to neutralize the system until the charge
> becomes '0'. Can you suggest me what is going wrong, or if it is
> okay??

If you were to 'check ang' before adding ions, the charge would
presumably not be integral, e.g. .97041 after the decimal. Do you
have any non-standard residues that might have a non-integral
charge? Leap adds ions with integral charge and thus the solute
must have integral charge to arrive at 0.

Bill
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