Dear Abinaya,
If you would like to do this the standard way (ignoring cavities), I
recommend reading through one of the amber tutorials:
http://ambermd.org/tutorials/basic/tutorial1/
and also look at the "LEaP" section of the ambertools manual.
The problem with the "standard" way is that it does not properly solvate
the biomolecular cavities. I have written a program that does this but you
must
first become familiar with the "standard" way in order to understand how it
works.
Once you have learned the standard method, please look at my tutorial for
obtaining the solvent distribution within the biomolecule:
http://sites.google.com/site/dansindhikara/Home/software/placement/tutorial
If you have any questions with the "Standard" tutorial, please send them to
the amber reflector: amber.ambermd.org
If you have questions regarding my method please e-mail me directly.
I hope this helps and good luck with your simulation.
-Dan
On Mon, Jan 2, 2012 at 3:11 PM, abinaya raju <abi1509.gmail.com> wrote:
> Respected Sir,
>
> I am very much new to amber 11. Can you give me some
> guidelines as to how we can solvate a protein and add ions using amber 11
> or ambertools 1.5?
>
> Thanking you,
> Yours sincerely,
> Abinaya
>
> --
> Abinaya Raju,
> IV year, B.Tech, Bioinformatics,
> SASTRA University,
> Thanjavur,
> Contact No:+91-9962937493
>
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Sun Jan 01 2012 - 23:00:03 PST
