Hi Fernando,
To prepare your protein i.e to add hydrogens and determination of
protonation state you can use H++ server (
http://biophysics.cs.vt.edu/H++/). You can specify the pH at which you
want to determine the protonation
state. For missing residues you can use the Modeller./Swiss 3D.
On Tue, Apr 12, 2011 at 10:30 PM, Fernando Blanco <amberfbv.gmail.com>wrote:
> Dear Amber Users
>
> I am going to start a new Project studying Protein-Coactivator
> Interactions.
>
> I would like to carry out MD and FEP calculations with AMBER
> but i have not experience
>
> I am working with the tutorials, but anyway I have several doubts
>
> My first goal is set up a good protocol to fit the protein:
>
> 1. Adjust hydrogens and protonation state
> 2. Correct the lost aminoacides
> 3. ...
>
> i.e. make all the preparation steps to have a good model for the following
> studies
>
> Could anybody give me any orientation/recommendations?
>
> Thank you so much
>
> Fernando Blanco
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Received on Tue Apr 12 2011 - 23:30:03 PDT
