AMBER Archive (2007)

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

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Mon Jan 22 2007 - 20:10:47 CST

Hi Bill

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.

Thanks for help. Best Regards
Akshay Patny (Olemiss)

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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
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-----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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