Re: AMBER: Charges in TI calculations and leap

From: David A. Case <>
Date: Tue, 30 Jan 2007 13:24:33 -0800

On Tue, Jan 30, 2007, Austin B. Yongye wrote:

> The overall charge of the ligand is zero, and I am using explicit solvent.
> I here is a snippet of my perturbation file:
> ....
> set lig.4.1 pert true
> set lig.4.2 pert true
> ....
> set lig.4.1 pertName C1
> set lig.4.1 pertType CG
> set lig.4.1 pertCharge -0.0410
> set lig.4.2 pertName H1
> set lig.4.2 pertType H2
> set lig.4.2 pertCharge 0.0000
> ....
> solvatebox lig TIP3PBOX 8
> saveamberparmpert lig abc_inwat.crd
> Looks like the "charge" command reads the input after pertCharge as Qs,
> not deltaQs. This input format was adopted from AMBER8 and later versions,
> but the "charge" routine has not been modified accordingly.

Try using the xleap editor to modify the charges; I think that will work.
We'll look into the problem with the "set" command (or maybe you already have,
and can recommend a patch(?).

Are you sure that you can't updage to Amber 9? Everything about "perturbed"
this and that goes away in the newer versions. We still try to provide
support for old versions of Amber, but fixing problems that are unique to the
old version (and don't exist in the current version) is likely to get lower


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Received on Wed Jan 31 2007 - 06:07:43 PST
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