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.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On
Behalf Of Bill Ross
Sent: Monday, January 22, 2007 7:58 PM
To: amber.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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Received on Wed Jan 24 2007 - 06:07:30 PST
