Hi Christina,
Thanks very much, we will try your way to first strip off all the mobile
ions, and keeping the bound ones and then run MMPBSA.py. Thanks for the
paper.
Nanjie
On Thu, Dec 6, 2018 at 8:34 AM Christina Bergonzo <cbergonzo.gmail.com>
wrote:
> Hi,
>
> We did analysis like this for RNA bound Mg2+ ions in a 2017 paper:
> https://www.sciencedirect.com/science/article/pii/S000634951730629X
> I found that getting MMPBSA.py 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 MMPBSA.py 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.
> You can just strip all water and other ions out of your system before
> running MMPBSA.py, 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.
>
> -Christina
>
> On Thu, Dec 6, 2018 at 3:11 AM Keiran Corbett <keirancorbett.gmail.com>
> wrote:
>
> > What commands are using to include the ions?
> >
> > On Wed, 5 Dec 2018 at 21:27, Nanjie Deng <nanjie.deng.gmail.com> wrote:
> >
> > > We are trying to run MMPBSA.py 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 MMPBSA.py 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
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> > >
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> >
>
>
> --
> --------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> NIST/IBBR NRC Postdoctoral Researcher
> --------------------------------------------------------------
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nanjie Deng, Ph.D.
Assistant Professor
Department of Chemistry and Physical Sciences
Pace University
1 Pace Plaza, Room W337
New York, NY 10038-1598
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Received on Thu Dec 06 2018 - 20:00:02 PST
