AMBER Archive (2007)

Subject: Re: AMBER: Charges in TI calculations and leap

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jan 30 2007 - 13:48:00 CST

Can you describe the problem a little bit more? For instance, do u use
explicit solvent; if u add counter ions; how u perturb the charges, etc...

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

> Dear amber users,
> I am employing AMBER8 to perform TI calculations for carbohydrate ligands.
> When the charge perturbation file is read by the "charge" routine in leap,
> it seems that the charges are read as Qs, not as deltaQs. This leads to a
> wrong output for the perturbed charges.
> For example, when I perturb the charges on internal residues, and run the
> "charge" command in tleap, the total unperturbed and perturbed charges are
> reported as 0.0000. When I perturb charges on a terminal residue, and run
> the "charge" command, the total unperturbed charge is +0.194, but the
> perturbed charge is reported as 0.0000.
> Thanks,
> austin-
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-- 
  Ilyas Yildirim
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