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?
D L Senal Dinuka
College of Chemical Sciences
Institute of Chemistry Ceylon
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