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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Received on Thu Dec 06 2018 - 00:30:02 PST
