[AMBER-Developers] [sangita.imtech.res.in: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom]

From: David A Case <david.case.rutgers.edu>
Date: Tue, 11 Aug 2015 07:51:45 -0400

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?


AMBER-Developers mailing list
Received on Tue Aug 11 2015 - 05:00:05 PDT
Custom Search