AMBER Archive (2005)

Subject: Re: AMBER: problem with addIons

From: David LeBard (david.lebard_at_asu.edu)
Date: Wed Jul 06 2005 - 17:08:35 CDT

Hi ThuZar,

The paragraph description in the manual (Amber8, p.51) for the addIons
procedure says the following:

"This procedure is not guaranteed to globally minimize the electrostatic
energy. When neutralizing regular-backbone nucleic acids, the first
cations will generally be placed between phosphates, leaving the final
two ions to be placed somewhere around the middle of the molecule."

So, you may have to minimize the system first before the ions are in the
correct places.

Hope this helps.

Best,
David

On Wed, 2005-07-06 at 14:41, Lwin, ThuZar wrote:
> Dear Amber users,
>
> My protein has a negative charge of -8. When I neutralize this system as
> addIons protein Na+ 0
> all the sodium ions are added to one corner of the solvation box. I tried it on different machines, and it still does the same behaviour.
> Lastly, I downloaded the pdb file from amber8 tutorial
> 1PLC.inpcrd.pdb
> this pdb also shows ions at one corner.
> Isn't counter ions supposed to be scattered and appear near the charged residues like they appear in DNA? Why isn't addIons working for the case of proteins? Or am I doing something wrong?
>
> Thanks,
> ThuZar
>
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