AMBER Archive (2009)

Subject: Re: [AMBER] MMPBSA on a selected region

From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Dec 10 2009 - 13:15:58 CST

Hello,

This paper, http://www.springerlink.com/content/gh2801w6177v6881/ ,
describes how to do this with amber. It is a slightly different
technique, in which they include a "buffer" region around the active
site that doesn't move to stabilize the minimization some, the details
are described in the paper. The paper also includes a website with
detailed instructions:
http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html . Hopefully this
has the information you're looking for.

Good luck!
Jason

On Thu, Dec 10, 2009 at 1:20 PM, <ERIK.LAURINI_at_phd.units.it> wrote:
>
> Dear Amber users,
> I have a question about MMPBSA with AMBER9. I would define a sphere of 15 Angstrom from my ligand on which calculate entropy contribution. In this way I'll reduce the memory requirement because my system is too big, therefore it's not possible calculate entropy with nmode on all complex. I start from a complete (ligand, receptor, ions, solvent) .mdcrd file.  How can I do it?
> Any help will be welcome!!!!
>
> Best regards
>
> -erik-
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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