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

From: David A. Case <>
Date: Thu, 24 Feb 2005 18:31:04 -0800

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.

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

You can use the "desc" command 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. 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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Feb 25 2005 - 02:53:02 PST
Custom Search