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

From: Ray Luo via AMBER <amber.ambermd.org> Date: Mon, 8 Jan 2024 10:38:38 -0800

--
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 Mon, Jan 8, 2024 at 7:57 AM Yang, Li-Yen <zoeyxyang.gatech.edu> wrote:
> Hi Ray,
>
>
>
> Thank you so much for your response!
>
>
>
> As in my first email, I have also tried radiopt = 0.
>
> This is the pbsa.mdin file I have:
>
> 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 ???
>
>
>
>
>
>
>
> I’m not sure if the error is related to the radii settings in tleap.
>
> Could you please elaborate on how the tleap should be set up for EP types?
>
>
>
> Thanks a lot!
>
>
>
> Best,
>
> Zoey
>
>
>
>
>
>
>
>
>
> *From: *Ray Luo <rluo.uci.edu>
> *Date: *Friday, January 5, 2024 at 11:52 PM
> *To: *Yang, Li-Yen <zoeyxyang.gatech.edu>, AMBER Mailing List <
> amber.ambermd.org>
> *Subject: *Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius
> assigned for atom
>
> 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
> <https://urldefense.com/v3/__http://prod.nc__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Ijz2H7hr23GIgOUFpjFmVoyYqlrk8ulsrkd0pCaHzc9TrDxdkew2bt6nZQEduZEUQjgb8cd7-tuT3zIYFQ$>
>
> 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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