Hello,
If you are using amber10 or amber11, a good choice would be a "generalized
distance" coordinate. Since Amber10, you can impose restraints resulting
from a linear combination of up to 4 distances. See the first section of
the Chapter on NMR restraints in the Amber manual (in the Amber11 manual,
it's chapter 6). This will tell you how to set up your restraint file. You
have to think about how you will set up the linear combination, though,
since you want to obtain a range of values that you can scan such that you
know you are going from your reactants to product/intermediates. This
approach will give you a 1-D curve (with the y-axis being energy).
Another option would be to define 2 different restraints and scan along both
independently (both restraints can be put in the same restraint file, one
after the other). This approach would give you a 2-D surface (plotted in
3-D, with the z-axis being energy), but is far more expensive
computationally since you need to compute more points.
Hope this helps,
Jason
On Wed, Aug 4, 2010 at 2:09 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> I am trying to study a SN2 reaction of an ezyme. The putative reaction
> coordinates should be the nucleophilic addition of hydroxide (O) nucleophile
> to the carbonyl carbon (C) and the elimination of the leaving group (N)
>
>
> Thus the reaction coordinate should be defined as R(O-C) - R(C-N), where
> R(O-C) and R(C-N) are the distances between the center (C) to the binding
> group (O) and leaving group (N) respectively.
>
>
>
> In the restrainst file I know how to define single distance restraint, e.g.
> as follows:
>
>
> #Distance restraint between O and C
>
> &rst iat=575,600, r1=.0, r2=2.0, r3=2.0 r4=100.0, rk2=20.0, rk3=20.0,
> iresid=1,
> ATNAM(1)="O'",
> ATNAM(2)="C'" /
>
>
> I also know I can also define the second distance between C and N by adding
> the same lines for O-N bond.
>
>
>
> However, should I define them in the same restraint file? If it is in the
> same file, I will only get one result file, and the PMF can only read the
> first line only. However, it did not seems to be what I want.
>
>
>
> Could you mind to share your experiences with me how to define a restraint
> coordinate for a SN2 reaction?
>
>
>
> Many thanks in advance,
>
>
>
> Catherine
>
>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Aug 04 2010 - 06:00:10 PDT
