Re: AMBER: AMBER sander

From: David A. Case <>
Date: Fri, 14 Sep 2007 17:50:47 -0700

On Fri, Sep 14, 2007, Eduardo Mendez wrote:

> I have to quickie questions. I can not tell how to solve these issues
> from the manual :(
> a) Can I save the final configuration on PDB format after a sander
> simulation?. How?.

See "ambpdb".

> b) I want to simulate a protein in water, but would like to combine
> implicit/explicit method. should I try to put constrains in the
> waters so these dont swim away from the surface of the protein?. ( I
> need to see if a water enters a cavity).
> Is it reasonable to mix explitic/implicit this way?

It might be possible to do something like this, but it would a research topic
in itself to figure out how, and it is certainly has no "quickie" answer.
I would think that one would need a lot of experience with simulations, and
some familiarity with the code, before tackling a problem like this.


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Received on Sun Sep 16 2007 - 06:07:45 PDT
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