Yes counterions are removed unless participating in binding... i.e. forming
a bridge between your ligand and receptor.
Oliver
On 9 July 2010 12:14, Catein Catherine <askamber23.hotmail.com> wrote:
>
> Dear
>
>
> Do I have to keep the Na+ counterions in prmtop and snapshot generation
> when I do mmGBSA/PBSA calculation?
>
>
>
> I have done a calculation on a protein-drug system, for my MD calculation,
> 20 salts and 20000 water molecules were added. However, when finish the
> calculation. I want to calculate the mm-pbsa/gbsa energy. I understand I
> need to exclude all the water molecule in extract snapshot and prepare free
> of water prmtop files for energy.mmpbsa. How about the counterions that I
> added? Should I also exclude all them in the snapshot and energy
> procedures?
>
>
>
> Best regards,
>
>
>
> Cat
>
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Received on Fri Jul 09 2010 - 04:30:06 PDT
