Re: [AMBER] Include bound ions as part of the receptor molecule in

From: Christina Bergonzo <>
Date: Thu, 6 Dec 2018 08:34:21 -0500


We did analysis like this for RNA bound Mg2+ ions in a 2017 paper:
I found that getting to recognize the ions as part of the binding
site was problematic, since ions exchange and couldn't be specified by
residue numbers.

If this is the case with your system too, the CPPTRAJ scripts in the
supporting information of that paper will help you to do the following:
1. find the closest ion to each binding site, and then
2. strip the original trajectory based on this distance criteria, so that
you get your solute of interest plus the bound ions for each frame.

Then I ran using the stripped trajectory and the designations for
the receptor and ligand mask would include the ion residues (now constant
since they are the only 2 ions left).

Of course, you will need to create topology files for the solute + 2 ions
(or however many you have) to run the analysis.

If your case is that the ions never exchange, then it is even easier for
You can just strip all water and other ions out of your system before
running, giving it an appropriate topology file for this as well.

Hope this helps, please let me know if you have any more questions as to
how we did this.


On Thu, Dec 6, 2018 at 3:11 AM Keiran Corbett <>

> What commands are using to include the ions?
> On Wed, 5 Dec 2018 at 21:27, Nanjie Deng <> wrote:
> > We are trying to run in Amber18 on a DNA-ligand-ion complex
> > trajectory. There are two bound K+ ions inside the DNA which we want to
> > include as part of the receptor molecule in the MMPBSA analysis. However,
> > the script always automatically treating the two ions as part
> of
> > the solvent and excluding them in the calculation, even as we explicitly
> > define receptor_mask to include the ions. Are there other work around to
> > include the ions in the MMPBSA post-processing in Amber?
> >
> > Thanks.
> >
> > --
> > Nanjie Deng, Ph.D.
> > Assistant Professor
> > Department of Chemistry and Physical Sciences
> > Pace University
> > 1 Pace Plaza, Room W337
> > New York, NY 10038-1598
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
> _______________________________________________
> AMBER mailing list

Christina Bergonzo
Research Chemist
NIST/IBBR NRC Postdoctoral Researcher
AMBER mailing list
Received on Thu Dec 06 2018 - 06:00:02 PST
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