Hi Jim,
Thanks for your response.
Sorry for the naïve question as I’m new to the field.
Could you please elaborate on how I should use OPC3 in the pbsa.mdin file?
Thanks!
Zoey
From: James Kress via AMBER <amber.ambermd.org>
Date: Saturday, January 6, 2024 at 12:47 AM
To: 'AMBER Mailing List' <amber.ambermd.org>
Subject: Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom
How about using OPC3?
Jim Kress
-----Original Message-----
From: Ray Luo via AMBER <amber.ambermd.org>
Sent: Friday, January 5, 2024 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
>
> 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-stag
> e-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-stag
> e-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 Mon Jan 08 2024 - 09:00:03 PST
