AMBER Archive (2006)

Subject: Re: AMBER: dummy atoms in MMPBSA

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Jul 27 2006 - 07:18:01 CDT

Dear Andrea,

Definitely it is affecting the results. I have done some simulations using
GB approach with and without dummy atoms. Normally a dummy atom should not
affect the energy values, but because of the calculation of the solvent
accessible surface area will include the dummy atom, it will. The EGB
terms with/without dummy atoms were different in my test cases.

Moreover, I dont think that someone can use implicit solvent approach with
TI in Amber 8 (if there are dummy atoms in both states). Amber 9 is
working, except the problem I described above. I am trying to play with
the source code to solve this problem, but if anyone gave any thoughts
about this issue, I will be happy to hear their ideas/suggestions.

Best,

On Thu, 27 Jul 2006, Andrea Bortolato wrote:

> Dear all,
>
> I am doing TI and MMPBSA studies on a set of inhibitors.
>
> I was wondering if the presence of dummy atoms (necessary for the TI) can
> influence the results of MMPBSA study, for example the solvent-accessible-surface-area.
>
> Many thanks,
> Andrea Bortolato
>
>
> ---------------------------------------
> Andrea Bortolato, Ph.D. Student
>
> Molecular Modeling Section
> Department of Pharmaceutical Sciences
> University of Padova,
> Via Marzolo, 5
> 35131 Padova - ITALY
> Phone: +39-049-8275801
> Fax: +39-049-8275366 or +39-049-8275704
> e-mail:andrea.bortolato.1_at_unipd.it
> Webpage URL http://mms.dsfarm.unipd.it
> ----------------------------------------
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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