AMBER Archive (2007)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jan 23 2007 - 11:30:06 CST

> I have an organic ligand for which the charge is >>>
>
> > check TEL
> Checking 'TEL'....
> WARNING: The unperturbed charge of the unit: 0.999960 is not zero.
> Checking parameters for unit 'TEL'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 1
> Unit is OK.
>
> Should this be a problem? I want to simulate the system with the
> organic ligand charged.

I forget if there's a 'fudge factor' when neutralizing with ions.
This is pretty close to integral charge. If you can get it to 1.0
that could neutralize worry :-) If you don't want to neutralize it
with an ion, I doubt it's a problem. Otherwise try and see if it
gets neutralized.

Bill

>
> Thanks for help. Best Regards
> Akshay Patny (Olemiss)
>
> = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
> Akshay Patny
> PhD Candidate (5th Yr.), Computational Chemistry
> Department of Medicinal Chemistry, School of Pharmacy
> The University of Mississippi
> 805 College Hill Rd, # 9, Oxford, MS 38655
> E-mail: akshay17_at_olemiss.edu
> Phone (O): (662)-915-1286,(M): (662)-801-5496
> = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
> Behalf Of Bill Ross
> Sent: Monday, January 22, 2007 7:58 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: ADDIONS do not neutralize to ZERO
>
> >> 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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