AMBER Archive (2008)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Nov 13 2008 - 14:39:41 CST

On Sun, Nov 09, 2008, E.M. wrote:
>
> 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 don't see any of this in my tests. So, we need exact details, not just
"I built a protein", but which protein, which force field libraries, which
leap commands, etc. See if you can make a minimal test case that illustrates
the problem.

[And, since perturbed charges are not used anymore, this might be innocuous,
but it might also point to some other problem.]

...dac

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