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, (1lambda)^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 12 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
>
> 
> The AMBER Mail Reflector
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>

Ilyas Yildirim

 Department of Chemisty  
 University of Rochester  
 Hutchison Hall, # B10  
 Rochester, NY 146270216  Ph.:(585) 275 67 66 (Office) 
 http://www.pas.rochester.edu/~yildirim/ 


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