Yes. We attempted to do this "per-partes" approach in:
M.Orzechowski, P.Cieplak, L.Piela
Theoretical Calculations of the Coiled-Coil Stability in Water
in the Context of its Possible Usage as a Molecular Rack
J.Comput.Chem. 23,106-110, (2002).
Best
Piotr
On Fri, 27 Feb 2009, Marek Malý wrote:
> From: "[iso-8859-2] Marek Malý" <maly.sci.ujep.cz>
> Sender: amber-bounces.ambermd.org
> To: amber.ambermd.org
> Date: Fri, 27 Feb 2009 19:21:29 +0100
> Subject: [AMBER] Partial entropy calculations ?
> Reply-To: AMBER Mailing List <amber.ambermd.org>
>
> Dear amber users,
>
> I would like to know if there is any possibility how to calculate entropy
> change (complexate X noncomplexate state) in the case
> of relatively big complexes (cca 15k atoms), like for example high generation
> dendrimer + oligonucleotide - please see the attached picture.
>
> I didn't succeed with direct calculation of the whole complex entropy due to
> the enormous RAM memory requirements (36 GB).
> At the end I tried it with NAB on the PC with 32 GB RAM but my calculation
> was interrupt after 4 days without finishing the entropy calculation.
> (only minimisation was done).
>
> So my question is: is it possible to calculate entropy of the whole complex
> using some "Per-Partes" methodology or is it
> possible to at least calculate (as an sufficient approximation) just the
> entropy of some relevant specific region (in my attached picture the green
> part).
>
> If this is not available in Amber ( using MM-PBSA, NAB ) does anybody know
> about some another software where is possible to realize such calculations ?
>
> Thanks in advance for any relevant information/directions.
>
> Marek
>
>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
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Received on Sat Feb 28 2009 - 08:49:52 PST
