AMBER Archive (2004)

Subject: Re: AMBER: FEP - GIBBS of charged sidechains using IELPER

From: David A. Case (
Date: Sun Nov 28 2004 - 17:28:43 CST

On Sun, Nov 28, 2004, Annette H?glund wrote:
> There was some recent discussions about perturbing a charged sidechain
> using the IELPER (electric decoupling) option.
> One thing is still unclear to me:
> Two legs are needed:
> a: perturb only the charges of the sidachain atoms during A -> A'
> b: perturb the atoms to dummy atoms (vdW (and what is rest of the charge
> as well?)) during A' -> B
> The question:
> Is the A' the output from the first 1 -> 0 (lambda) perturb and then A'
> (.crd) is used as input for a second 1 -> 0 perturbation?

This is correct: it is like having two completely separate calculations,
whose deltaG values you add together to get the final result.

....good luck...dac

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