AMBER Archive (2005)

Subject: Re: AMBER: Does delta.charge mean "final charge" for a dummy atom?

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Fri Feb 25 2005 - 18:38:05 CST

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Thu, Feb 24, 2005, Eric Hu wrote:
>
> > I edit the delta charges for a perturbation so
> that
> > the final molecule has a total charge of 1.0 while
> the
> > inital molecule has a total charge of 0.0. The
> > hydroxide group disappearing during the simulation
> has
> > a net charge of -0.743207. So I set the delta as
> > 0.743207 and atom types for oxygen and hydrogen as
> DO
> > and DH. However when I try to save the top and crd
> > files, leap gives an error message: "the perturbed
> > charge: 1.494397 is not integral." Interestingly
> if I
> > reset the delta as the original -0.7743207,
> everything
> > seems fine.
>
> This is a case where you need to tell us what you
> actually did, not what you
> intended to do. Saying "I set the delta as 0.74" is
> not really much help,
> since I can't tell what "the delta" is: there is a
> separate value for every
> atom in the molecule.
>

xleap-->edit mol-->edit selected atoms-->delta.charge
Name Type Charge Element Pert.name Pert.type Delta.charge
...
O45 O -1.0975 O O45 DO -1.0975
H46 HO 0.3503 H H46 DH 0.3503

works as previously discussed.

Name Type Charge Element Pert.name Pert.type Delta.charge
...
O45 O -1.0975 O O45 DO 1.0975
H46 HO 0.3503 H H46 DH -0.3503

gives an error message "the perturbed charge: 1.494397 is not integral."

> Also, be sure to specify which version of Amber you
> are using.
>
Amber 8.0

> You can use the "desc" comm
and to see the charges on
> your molecule, and you
> can add them up manually to see what you get. You
> should definitely make sure
> that the charges that leap is using are the ones you
> really want.
Yes

>And it's
> often a good idea to set up and run a least a short,
> ordinary (non-TI)
> simulation for both the initial and final states, so
> that you can satsify
> yourself that both the intial and final potentials
> are acting in the way you
> want them to.
>
> ...good luck...dac
>
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