AMBER Archive (2008)

Subject: RE: AMBER: using NAB to calculate entropy. .

From: Wang, Xuelin (Xuelin.Wang_at_stjude.org)
Date: Wed Feb 06 2008 - 15:00:46 CST

Dr. Case,

How can I incorporate NAB to the MM_PBSA calculation (in NMODE part) or
I have to use NAB independently?

Thanks
Nick

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Wednesday, February 06, 2008 2:21 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: using NAB to calculate entropy. .

On Wed, Feb 06, 2008, Wang, Xuelin wrote:
>
> Is there any information about how to use NAB to calculate entropy of
> ligand-protein systems? My complex is too big for NMODE calculations.

NAB reports thermodynamics from normal mode calculations just like nmode
does.
So, you just take snapshots, minimize and compute modes in the same way,
then average the results from the various snapshots. It should be
pretty
simple to modify mm-pbsa or pyAmber to handle the averaging, or you can
just
do it by hand.

...regards...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  skype:                 dacase
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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