AMBER Archive (2008)

Subject: Re: AMBER: AMBER question: perturbed charge twice the unperturbed

From: E.M. (pckboy_at_gmail.com)
Date: Sun Nov 09 2008 - 17:08:05 CST

Cheers David

I built a protein with the resulting charge of -22
I used
addIons2 CMPLX Na+ 0
to add charges to the system,
and I got:
> charge CMPLX
Total unperturbed charge: -0.9998
Total perturbed charge: -1.9996
>
In tleap. Initially the "unperturbed" charge was -22.9998 and the
perturbed one was -44.99998 or something like that
I am using amber9
and I do not understand what it means

Eduardo

David A. Case wrote:
> On Sat, Nov 08, 2008, Edward M wrote:
>
>
>> I was just wondering why the unperturbed charge is one half of the perturbed
>> one (or the other way around).
>>
>
> Details? Charge of what?? How was it constructed? [Note that current
> versions of Amber no longer make use of "perturbed charges". Even in the
> past, what you describe would not be a general feature.]
>
> ...dac
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