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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Received on Tue Aug 03 2010 - 23:30:05 PDT
