Dear Dr. Miller
Thank you for your help. I got it now.
But, my zinc ion radius is 1.1 (as in my zinc frcmod file), and when I searched under %FLAG RADIUS_SET for this number in prmtop file of my enzym, I couldn't find it.
What does it mean?
Sorry for any disturbance.
Thanks in advance
S. Bill
--- On Sun, 14/2/10, Billy Miller III <brmilleriii.gmail.com> wrote:
From: Billy Miller III <brmilleriii.gmail.com>
Subject: Re: [AMBER] mmpbsa.py ion radius
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Sunday, 14 February, 2010, 2:25
MMPBSA.py does not read any parameters that are placed in any of the files
related to mm_pbsa.pl. MMPBSA.py sets radiopt=0 by default for PB
calculations, which means that the atomic radii are taken directly from the
prmtop files specified by the user. This means that MMPBSA.py is using the
zinc ion radius that you set when you created the prmtop files using leap.
I hope that helps.
Good luck!
-Bill Miller III
On Sat, Feb 13, 2010 at 9:02 PM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBERI am a little bit confused and I hope you may help me.When I used
> MM-PBSA (old version), it complained about missing radius for zinc ion so I
> have implemented the zinc ion radius in mm_pbsa_calceneent.pm file.But,
> when I used MM-PBSA.py (new version), it didn't complain about zinc radius,
> why? Does it read the zinc radius from mm_pbsa_calceneent.pm file?Thanks
> in advanceS. Bill
>
>
>
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Received on Mon Feb 15 2010 - 10:30:02 PST
