AMBER Archive (2009)

Subject: Re: [AMBER] MMGBSA error

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Dec 25 2009 - 16:17:26 CST

On Fri, Dec 25, 2009, Jason Swails wrote:
>
> It would appear the only reason there's a "virtual box" needed for the
> minimization is that it's using ewald... I'm not sure why an ewald
> parameter is set, since nmode is calculating gas phase vibrational
> entropies anyway. Perhaps removing the &ewald namelist in the
> minimization input will fix your problems...

This explanation is not correct. Basically, sander (in its current
incarnation) is not designed to do vacuum minimizations. It tries to trick
the system into thinking it is periodic, solely for the purpose of using
the list generator designed for periodic systems.

It would be better for the mm_pbsa scripts (new or old, perl or python)
to set up minimzation scripts using a nab script (something like
amber11/test/nab/txmin.nab). For now, you should visualize your system before
and after minimization, to try to see what is going wrong...it looks like it
is changing shape drastically upon minimization. If so, the minimization (and
any subsequent normal mode calculations) are not going to do you much good in
an MM-PBSA context.

...dac

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