Re: AMBER: Re: TI tutorial

From: David A. Case <>
Date: Tue, 28 Jun 2005 08:49:53 -0700

On Tue, Jun 28, 2005, Jiten wrote:
> Now looking at the first simple example (charging free energy calculation),
> the PERT.type is same with the TYPE, therfore the perturb charge will not
> be affected. Is it a mistake or the PERT.type shoulb be kept similar with
> what is given in the 2nd example.
> [In amber8 manual : An atom isconsidered to be perturbed if its PertType is
> different than its Type.]

Did you read the full paragraph you are quoting (p. 34, top)? Immediately
after the sentence that you quote it says:

"The upshot of this is that you can change the charge of an atom without
making the atom become "perturbed". This fits how sander works: energies with
the perturbed charges are always used (if needed) independent of which atoms
(if any) are marked as "perturbed".

I suppose it could be clearer, but it seems to cover exactly the question you

....good luck...dac

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Received on Tue Jun 28 2005 - 16:53:00 PDT
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