AMBER Archive (2009)

Subject: Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB.

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jan 21 2009 - 08:52:33 CST

On Wed, Jan 21, 2009, Marek Mal? wrote:
>
> From your responses clearly follow that memory requirements (for N-R
> minimisation and normal mode analysis) are strongly
> dependent on quality of the previous conjug. grad. minimistation or more
> precisely on the size of the "frms".

No: the memory requirements are independent of frms. It is just that NR
minimization (as coded here) requires a good starting point.

> OK in mm_PBSA is possible to choose between PB and GB algorithms to
> calculate desolvation energy. I always used PB
> since I read somewhere that it is let say more realistic model but if I
> am not wrong in NAB is available only GB
> in this moment so what is the better choice (from the point of view of
> more realistic results).

PB is generally preferred for "snapshot" analysis. The recommendation
for NAB is only for the normal mode calculations -- other parts of the
calcualations can use other programs.
>
>
> #1 - to use mm_PBSA for the enthalpic contribution with PB method to
> calculate desolvation energy and
> than to use NAB with gb=1 to calculate entropic contribution.

The above is what I recommend. No matter what you do, the entropy part
will be dicey.

...dac

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