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Hello all,
I have proposed a different question earlier relating to the above subject
and managed to model my non-standard sugar and run a simulation
successfully. As per now, I have a doubt as to did I model properly.
Because my structure is a transition state implying the properties of a
non-standard sugar ie. a glucose molecule with anomeric -O connected to a
cyanogenic moiety. Thus I modeled the cyanogenic portion with a separate
parameter file (frcmod) and provided GLYCAM_06j-1 for the sugar portion
(named and numbered correctly). Yet as per my understanding GLYCAM
forcefield describes equilibrium bond and angle parameters (of a chair
conformer) which is in my case a transition state (slightly distorted
half-chair conformer). So my question is to clarify whether the above
argument is true or not.
Are we supposed to generate a whole set of novel forcefield parameter for
simulating the transition states?

Thank you

-- 
D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Rajagiriya
Sri Lanka
+94 77 627 4678