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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Wed, Aug 20, 2014 at 2:36 PM, Jason Swails <jason.swails.gmail.com> wrote: > On Wed, Aug 20, 2014 at 4:29 PM, Vlad Cojocaru < > vlad.cojocaru.mpi-muenster.mpg.de> wrote: > >> In my experience inp=2 gives far better affinities than inp=1 for >> protein-nucleic acids . As long as non-linear PB is used and sasopt=2. >> Therefore I disagree with changing the default to inp=1. In fact I would >> argue MMPBSA should not run with any defaults as users need to understand >> every single parameter. >> > > Thank you for the feedback. Obviously, bad experiences with inp=2 are > over-expressed here, so it's good to hear the other side as well. > > I think eliminating the default for inp is probably the best way to go > here. And while I agree users should know all of the relevant parameters, > it's too much of a change to rip out all of the defaults, in my opinion. I > think we've learned that silently changing them is a bad thing, so in cases > where no clear "best practice" or "most common" choice exists, that value > should be specified explicitly. > > Thanks, > Jason > > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Aug 20 2014 - 17:30:02 PDT