Hi There, I am trying to run MDS over some docked result generated by Autodock4, but I am not sure of the forcefield I should use. If anybody have tried doing it before, please guide me for the same. For generating topology of ligand, I am using PRODRG server, which has limited option for forcefield. Also, how can I give the parameters for varying temperature of a particular group during the MDS, like how canI define the steps I want to vary it ?
waiting for some suggestion. With Thanks, Vivek
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