On Nov 29, 2011, at 8:21 AM, Lee Lior <lee.lior.nyu.edu> wrote:
> 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?
Hybridization is all but useless to leap. It uses it to do some (very) rudimentary minimizations prior to building the topology file, but it is in no way used during the creation of the topology file directly.
You should be fine ignoring this particular issue.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
>
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Received on Tue Nov 29 2011 - 06:30:03 PST
