Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Fri, 5 Jan 2024 20:51:38 -0800

Zoey,

Looks like you are invoking the default option of radiopt =1, which asks
the program to set radii inside the code, but it can't find anything for
the EP type (extra point, usually used for lone pairs on an atom). This is
because pbsa wasn't designed to handle force fields with EP types, though
we are working on extending pbsa for polarizable force fields with EP types.

In general, you'll need to be careful with the continuum solvent models and
force fields with EP types as these are not yet well studied.

If you want to give it a try, you'll need to set radiopt = 0 so it can use
radii in the prmtop file. Of course you'll need to make sure the radii for
EP types are set in tleap.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Fri, Jan 5, 2024 at 11:50 AM Yang, Li-Yen via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I have finished a constant ph simulation and I am trying to use pbsa to
> get the electrostatic potential.
>
> I am running the command pbsa -O -i pbsa.mdin -o pbsa.mdout -p
> complex.parm7 -c prod.nc
>
> The pbsa.mdin file is as follow:
>
> Sample PB visualization input
> &cntrl
>   inp=0
>   /
> &pb
>   npbverb=1, space=1., sasopt=2,
>   phiout=1, phiform=2
>   /
>
> It gave an error in the bottom of the pbsa.mdout file: PB Bomb in
> pb_aaradi(): No radius assigned for atom 11777  EPW   EP
>
>
>
> I saw a similar question in the mailing list, and they said to set inp=1
> and radiopt=0, so I tried the following pbsa.mdin:
> Sample PB visualization input
> &cntrl
>   inp=1
>   /
> &pb
>   npbverb=1, space=1., sasopt=2,
>   phiout=1, phiform=2,
>   radiopt=0
>   /
>
> But it gave the error:
>
> Fortran runtime error: Bad value during floating point read
> Error termination. Backtrace:
> #0  0x7ffff6221e18 in formatted_transfer_scalar_read
>             at
> /usr/local/pace-apps/spack/root/releases/v0.18/stage/fliu67/spack-stage-gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/spack-src/libgfortran/io/transfer.c:1650
> #1  0x7ffff62235d3 in formatted_transfer
>             at
> /usr/local/pace-apps/spack/root/releases/v0.18/stage/fliu67/spack-stage-gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/spack-src/libgfortran/io/transfer.c:2339
> #2  0x4166d3 in ???
> #3  0x4054cd in ???
> #4  0x407834 in ???
> #5  0x40787a in ???
> #6  0x7ffff57c0554 in ???
> #7  0x40201d in ???
> #8  0xffffffffffffffff in ???
>
>
> Any guidance would be greatly appreciated!
>
> Thanks!
> Zoey
>
>
>
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Received on Fri Jan 05 2024 - 21:00:02 PST