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

From: Ray Luo, Ph.D. <>
Date: Sun, 16 Aug 2015 11:16:18 -0400


This has been changed, i.e. the new atom types have been added to the
master branch. I'll check it in next week when I'm back in office.

If needed, I can also generate a patch for the 2015 release.

All the best,

Ray Luo, Ph.D.
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Aug 11, 2015 at 7:51 AM, David A Case <> wrote:
> Is there anything (reasonable) that we can do to avoid the following,
> increasingly common, problem report:
>  PB Bomb in pb_aaradi(): No radius assigned for atom 17 CB C8
> Should we do better at identifying proper radii based on atom type? (I'm
> assuming that "C8" is the problem here....)
> Could we force inp=1, and assign radii based on element?
> [As a related concern, the inp=2 model is even less "universal" than is
> inp=1; I'd like to consider returning to inp=1 as the default, and ask
> users wishing to use inp=2 to make sure their problems are similar to the
> ones on which the inp=2 model were tested.]
> Can we at the least give a more expansive error message?  Add a section to the
> Manual where we explain that Amber's GB model is not a universal one, and that
> you cannot just expect to carry out arbitrary MM-GBSA calculations?
> ...thx....dac
> _______________________________________________
> AMBER-Developers mailing list
AMBER-Developers mailing list
Received on Sun Aug 16 2015 - 08:30:04 PDT
Custom Search