If you have a distorted ground-state (such as may be present in a Michaelis complex, or a TS-like mimetic) then GLYCAM may handle it fine. There are no constraints that prevent ring flexion in GLYCAM. Classical force fields in general are unable to handle the partial bonds present in a true transition state. However, when you introduce new atom types or linkages, there is always a need to carefully examine the electrostatic model and the valence parameters.
Excuse the brevity, sent from iPhone
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
+94 77 627 4678