[gmx-users] Running MDS over docked poses

[vivek sharma]

 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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