: [AMBER] MMGBSA error

From: Zhongjie Liang <zjliang.mail.shcnc.ac.cn>
Date: Sat, 26 Dec 2009 12:30:00 +0800

Thanks, I got it!

: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org]
David A. Case
ʱ: 20091226 6:17
ռ: AMBER Mailing List
: Re: [AMBER] MMGBSA error

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.


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