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-- Ray Luo, Ph.D. Professor 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 <david.case.rutgers.edu> 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.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Sun Aug 16 2015 - 08:30:04 PDT