AMBER Archive (2006)

Subject: Re: AMBER: TI-FEP for ILE--->VAL.

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Aug 03 2006 - 01:15:10 CDT

What is your thermodynamic cycle? Doing just one part of the
cycle will not give u anything physical. In your thermodynamic cycle, the
dummy atom effects (bond angle, dihedral, etc.) will cancel at the end.

On Thu, 3 Aug 2006, Biswa Ranjan Meher wrote:

> Dear AMBER users,
>
> For our protein-drug system: we are doing the free energy perturbations in
> a transformation of ILE --->VAL using the TI method. We are using dummy
> atoms for the missing group -CH2 while transforming from ILE --> VAL.
>
> So in order to make the .frcmod file for the dummy atoms we need to
> have changes for the charges and Vdw parameters to zero.
>
> Regarding the force constants for bond, angle and dihedral parameters
> involving the dummy atoms - should it be same as in ILE?
>
> Since the bond, angle parameters and dihedral barriers are artificial for
> dummy atoms I am worrying if that can affect the free energy difference.
>
> Or should I put smaller values for those parameters just to keep the
> dummy atoms in place.
>
> I would appreciate your suggestion.
>
> Regards
> B.R. Meher
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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