AMBER Archive (2005)

Subject: Re: AMBER: Free energy pertubation (thermodynamic intergration)

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Apr 25 2005 - 15:43:36 CDT

Hi Matthew,

In order to do a perturbation from H --> NH2, you need to use 2 extra
dummy atoms in the initial (starting) structure. According to AMBER 8
Manual, this isnt possible. The reason is because of 'mixing' function
used in pp. 133. This function, (1-lambda)^k, does not have the first
derivative equal to zero at lambda = 0. As a result, it is not a smooth
transition function at the beginning (around lambda = 0). I have been
working on this problem for 1-2 month, and I have changed the source code
of amber, and replaced this function with something else, which will be a
smooth function at both ends; at lambda=0 and lambda=1. I have a test case
where I am transforming a methane molecule (CH4) to ethane (C2H6). As far
as now, the simulations are giving reasonable results. By that I mean the
following: I am doing a perturbation from eth --> meth and use the
trapezoidal rule to calculate the integral (pp.132l Eq.1). I do the same
thing for meth -> eth perturbation, and calculate the integral.
Theoretically, they should yield the same absolute value with a sign
difference. I am getting some expected results, but I am doing some other
simulations to see more about it.

I will write more about my results later, hopefully soon. Best,

On Mon, 25 Apr 2005 mrbroad_at_ilstu.edu wrote:

>
>
> hey guys~
>
> I am using AMBER 8 and trying to preform some FEP calculation on guanosine
> triphosphate and its analogs. I'm not sure however to make atoms appear.
> What I am specifically trying to do is change a (H) into an (NH2). I was
> guessing that I might have to make some dummy atoms, but I am not sure the
> proper way to do this. Any help is greatly appreciated.
>
> Matthew Broadus
>
> ------------------------------------------------------------
> Illinois State University Webmail https://webmail2.ilstu.edu
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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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