I am a graduate student in Suse Broyde's laboratory studying the
nucleotidyl transfer reaction. I have obtained a transition state by QM
methods that has the pentacovalent phosphorane intermediate upon addition
of the dNTP to the 3'O of the primer terminus. Thus my system include a P
atom with 5 P-O covalent bonds corresponding to sp3d hybridization. I
defined two new atom types, one for the pentacovalent phosphate and and the
second for two (out of the five) oxygen atoms with the abnormal properties.
The only problem I am facing now is that tleap doesn't recognize sp3d
hybridization. If I dont assign any hybridization, it shows in the leap log
that it uses sp0. Hence, I defined it as sp3.
Is this the right way to approach this?
Thanks,
Lee
**********************
Lee Lior-Hoffmann
PhD Graduate Student
Chemistry Department
New York University
lee.lior.nyu.edu
**********************
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Received on Tue Nov 29 2011 - 05:30:03 PST
