Re: [AMBER] RED vIII for Amber

From: Karl Kirschner <>
Date: Mon, 14 Dec 2015 08:42:54 +0100

Hi Anthony,

  I believe the way to do this is to manually include the following line
(as an example) in your RED input p2n file:

The 0.2 is the charge that you want to constrain atom #3 to have during the
fitting process. You can include as many of these lines as the number of
atoms that you want to keep the partial atomic charge constrained to.


On Sun, Dec 13, 2015 at 10:41 PM, Nash, Anthony <> wrote:

> Hi all,
> With the RED server having gone down, I know a link to the older version
> scripts (vIII) had been publicised in this Amber community. After looking
> through the various scripts, it seems relatively easy to set up on a local
> system with access to Gaussian. However, after carefully going through the
> only .pdf tutorial for vIII I didn't find anything to do with restraining
> the calculation of point charges to certain regions of an amino acid. If I
> recall correctly, the defunct online service allowed you to provide a
> project and system file. One of these files enabled the user to specify a
> list of atoms which would not contribute to the calculation of point
> charges (essentially capped ends to an amino acid backbone). Was this one
> of the differences between III and IV?
> I¹m getting the feeling I¹ll need to move back onto Antechamber.
> Thanks
> Anthony
> _______________________________________________
> AMBER mailing list

Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
AMBER mailing list
Received on Mon Dec 14 2015 - 00:00:03 PST
Custom Search