Re: [AMBER] positive free energy

From: Ray Luo, Ph.D. <>
Date: Wed, 20 Aug 2014 17:03:02 -0700

Frankly speaking, it's not straight forward to remove a default in the
python script. We probably need a new routine to check the presence of
the keyword in the input file and to drop a fatal bomb if it doesn't

Also, other essential options should also set no default values, such
as inp=1 surface tension/offset, atom radius definition, and solute
dielectric constant etc. These options influence the quality of the
mmpbsa method as well. Doing so would force people to think before
choosing whatever approaches/options.

Ray Luo, Ph.D.
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Wed, Aug 20, 2014 at 2:36 PM, Jason Swails <> wrote:
> On Wed, Aug 20, 2014 at 4:29 PM, Vlad Cojocaru <
>> 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
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Received on Wed Aug 20 2014 - 17:30:02 PDT
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