Hello,
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.
Regards
*Elvis Martis* PhD Student, Bombay College of Pharmacy
[image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in>
Website: http://www.elvismartis.in <http://www.elvismartis.in/>
group website: http://www.profeccoutinho.net.in/
Address:
Kalina, Santa Cruz [E]
, Mumbai, 400 098, INDIA
Alt. e-mail: emartis12.live.com
<
https://in.linkedin.com/in/elvisadrianmartis>
On 5 November 2016 at 17:44, Ramin Ekhteiari <ramin_ekh.yahoo.com> 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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>
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Received on Sat Nov 05 2016 - 06:00:02 PDT
