Re: [AMBER] positive free energy

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Wed, 20 Aug 2014 23:45:26 +0200

Maybe its worth mentioning in this thread that changing from inp=2 to inp=1 also involves changing other parameters such as cavity_surften and cavity_offset.

Best
Vlad

On August 20, 2014 11:36:44 PM CEST, 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.
>>
>
>‚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.
>
>Thanks,
>Jason
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
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>AMBER.ambermd.org
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-- 
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Received on Wed Aug 20 2014 - 15:00:04 PDT
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