Re: [AMBER] MM-PBSA calculation for HEME-contained protein

From: Elvis Martis <>
Date: Sat, 5 Nov 2016 18:12:36 +0530

Have you assigned PB radii during the preparation stage in leap?
If yes,
        Please check if you have kept RADIOPT=1, in your MMPBSA protocol
file, if yes then use RADIOPT=0.

If no,
the load your prmtop file in parmed and assign a suitable PB radii,
preferably mbondi3.


*Elvis Martis* PhD Student, Bombay College of Pharmacy
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On 5 November 2016 at 17:44, Ramin Ekhteiari <> wrote:

> Dear Colleagues,
> I'm running a MM-PBSA calculation for a HEME-contained protein using
> AmberTools16, but I'm facing with "PB Bomb in pb_aaradi(): No radius
> assigned for atom 7572 FE FE" error.
> Is there any advice to solve it?
> Your helps are really appreciated.
> Best regards,
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Received on Sat Nov 05 2016 - 06:00:02 PDT
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