Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation?

From: Mahmoud A. A. Ibrahim <m.ibrahim.compchem.net>
Date: Fri, 9 Jul 2010 12:29:37 +0100

Dear Catein
MM-PBSA script removes water molecules and ions automatically (strip_mask).
Sincerely;
M. Ibrahim


On Fri, Jul 9, 2010 at 12:14 PM, 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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                 Mahmoud A. A. Ibrahim
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Received on Fri Jul 09 2010 - 05:00:03 PDT
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