Re: [AMBER] positive free energy

From: Jason Swails <>
Date: Wed, 20 Aug 2014 17:36:44 -0400

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.

‚ÄčThank you for the feedback. Obviously, bad experiences with inp=2 are‚Äč
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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Aug 20 2014 - 15:00:03 PDT
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